Revision: 20895
http://sourceforge.net/p/jmol/code/20895
Author: hansonr
Date: 2015-12-20 22:01:37 +0000 (Sun, 20 Dec 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.4.1_2015.12.20"
code: (JavaScript) adding use of array.slice and implementing Java byte[] as
JavaScript Int8Array()
bug fix: array handling for labels very inefficient
bug fix: y = javascript("x") only creates string equivalent of x, not actual
numerical/object values
bug fix: y = javascript("x") draws "x" from wrapped anonymous function using
eval() instead of global context using window.eval()
Modified Paths:
--------------
branches/v14_4/Jmol/src/javajs/util/AU.java
branches/v14_4/Jmol/src/javajs/util/BS.java
branches/v14_4/Jmol/src/javajs/util/CompoundDocHeader.java
branches/v14_4/Jmol/src/javajs/util/PT.java
branches/v14_4/Jmol/src/javajs/util/Rdr.java
branches/v14_4/Jmol/src/org/jmol/applet/Jmol.java
branches/v14_4/Jmol/src/org/jmol/appletjs/Jmol.java
branches/v14_4/Jmol/src/org/jmol/jvxl/readers/IsoFxyReader.java
branches/v14_4/Jmol/src/org/jmol/jvxl/readers/IsoMOReader.java
branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
branches/v14_4/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java
branches/v14_4/Jmol/src/org/jmol/modelset/Atom.java
branches/v14_4/Jmol/src/org/jmol/script/SV.java
branches/v14_4/Jmol/src/org/jmol/script/ScriptMathProcessor.java
branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java
branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java
branches/v14_4/Jmol/src/org/jmol/shape/AtomShape.java
branches/v14_4/Jmol/src/org/jmol/util/GenericApplet.java
branches/v14_4/Jmol/src/org/jmol/viewer/AnimationManager.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
branches/v14_4/Jmol/src/org/jmol/viewer/SelectionManager.java
branches/v14_4/Jmol/src/org/jmol/viewer/StatusManager.java
branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
Modified: branches/v14_4/Jmol/src/javajs/util/AU.java
===================================================================
--- branches/v14_4/Jmol/src/javajs/util/AU.java 2015-12-17 22:22:22 UTC (rev
20894)
+++ branches/v14_4/Jmol/src/javajs/util/AU.java 2015-12-20 22:01:37 UTC (rev
20895)
@@ -36,46 +36,36 @@
/**
* Very important that this not be used with Int32Array or Float32Array,
- * because it is not initialized to all zeros in MSIE 9.
+ * because it is not initialized to all zeros in MSIE 9.
*
* @param array
* @param minimumLength
* @return array
*/
public static Object ensureLength(Object array, int minimumLength) {
- if (array != null && getLength(array) >= minimumLength)
- return array;
- return arrayCopyObject(array, minimumLength);
+ return (array != null && getLength(array) >= minimumLength ? array
+ : arrayCopyObject(array, minimumLength));
}
public static String[] ensureLengthS(String[] array, int minimumLength) {
- if (array != null && array.length >= minimumLength)
- return array;
- return arrayCopyS(array, minimumLength);
+ return (array != null && array.length >= minimumLength ? array
+ : arrayCopyS(array, minimumLength));
}
public static float[] ensureLengthA(float[] array, int minimumLength) {
- if (array != null && array.length >= minimumLength)
- return array;
- return arrayCopyF(array, minimumLength);
+ return (array != null && array.length >= minimumLength ? array:
arrayCopyF(array, minimumLength));
}
public static int[] ensureLengthI(int[] array, int minimumLength) {
- if (array != null && array.length >= minimumLength)
- return array;
- return arrayCopyI(array, minimumLength);
+ return (array != null && array.length >= minimumLength ? array :
arrayCopyI(array, minimumLength));
}
public static short[] ensureLengthShort(short[] array, int minimumLength) {
- if (array != null && array.length >= minimumLength)
- return array;
- return arrayCopyShort(array, minimumLength);
+ return (array != null && array.length >= minimumLength ? array :
arrayCopyShort(array, minimumLength));
}
public static byte[] ensureLengthByte(byte[] array, int minimumLength) {
- if (array != null && array.length >= minimumLength)
- return array;
- return arrayCopyByte(array, minimumLength);
+ return (array != null && array.length >= minimumLength ? array :
arrayCopyByte(array, minimumLength));
}
/**
@@ -132,22 +122,26 @@
}
/**
- * note -- cannot copy if array is null!
+ * note -- cannot copy if array is null! does not copy if length is unchanged
*
* @param array
* @param newLength
* @return array
*/
- public static Object arrayCopyObject(Object array, int newLength) {
- //System.out.println("ArrayUtil.copy " + newLength + " " + array + " ");
- if (array == null) {
- return null; // We can't allocate since we don't know the type of array
- }
- int oldLength = getLength(array);
+ public static Object arrayCopyObject(Object array, int newLength) {
+ int oldLength = (array == null ? -1 : getLength(array));
+ if (newLength < 0) newLength = oldLength;
if (newLength == oldLength)
- return array;
+ return array;
+ /**
+ * @j2sNative
+ *
+ * if (newLength < oldLength) return Clazz.newArray(-1, array, 0,
newLength);
+ */
+ {}
Object t = newInstanceO(array, newLength);
- System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
+ if (oldLength > 0)
+ System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
: newLength);
return t;
@@ -190,11 +184,16 @@
}
public static String[] arrayCopyS(String[] array, int newLength) {
- if (newLength < 0)
- newLength = array.length;
+ int oldLength = (array == null ? -1 : array.length);
+ if (newLength < 0) newLength = oldLength;
+ /**
+ * @j2sNative
+ *
+ * if (newLength < oldLength) return Clazz.newArray(-1, array, 0,
newLength);
+ */
+ {}
String[] t = new String[newLength];
if (array != null) {
- int oldLength = array.length;
System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
: newLength);
}
@@ -224,11 +223,16 @@
}
public static float[] arrayCopyF(float[] array, int newLength) {
- if (newLength < 0)
- newLength = array.length;
+ int oldLength = (array == null ? -1 : array.length);
+ if (newLength < 0) newLength = oldLength;
+ /**
+ * @j2sNative
+ *
+ * if (newLength < oldLength) return Clazz.newArray(-1, array, 0,
newLength);
+ */
+ {}
float[] t = new float[newLength];
if (array != null) {
- int oldLength = array.length;
System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
: newLength);
}
@@ -236,11 +240,16 @@
}
public static int[] arrayCopyI(int[] array, int newLength) {
- if (newLength < 0)
- newLength = array.length;
+ int oldLength = (array == null ? -1 : array.length);
+ if (newLength < 0) newLength = oldLength;
+ /**
+ * @j2sNative
+ *
+ * if (newLength < oldLength) return Clazz.newArray(-1, array, 0,
newLength);
+ */
+ {}
int[] t = new int[newLength];
if (array != null) {
- int oldLength = array.length;
System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
: newLength);
}
@@ -261,29 +270,49 @@
int oldLength = array.length;
if (n == -1) n = oldLength;
if (n == -2) n = oldLength / 2;
- n = n - i0;
- int[] t = new int[n];
- System.arraycopy(array, i0, t, 0, n);
- return t;
+ /**
+ * @j2sNative
+ *
+ * return Clazz.newArray(-1, array, i0, n);
+ *
+ */
+ {
+ n -= i0;
+ int[] t = new int[n];
+ System.arraycopy(array, i0, t, 0, n);
+ return t;
+ }
}
public static int[] arrayCopyRangeRevI(int[] array, int i0, int n) {
if (array == null)
return null;
- int[] t = arrayCopyRangeI(array, i0, n);
- if (n < 0)
- n = array.length;
- for (int i = n / 2; --i >= 0;)
- swapInt(t, i, n - 1 - i);
- return t;
+ /**
+ * @j2sNative
+ *
+ * return Clazz.newArray(-1, array, i0, n).reverse();
+ */
+ {
+ int[] t = arrayCopyRangeI(array, i0, n);
+ if (n < 0)
+ n = array.length;
+ for (int i = n / 2; --i >= 0;)
+ swapInt(t, i, n - 1 - i);
+ return t;
+ }
}
public static short[] arrayCopyShort(short[] array, int newLength) {
- if (newLength < 0)
- newLength = array.length;
+ int oldLength = (array == null ? -1 : array.length);
+ if (newLength < 0) newLength = oldLength;
+ /**
+ * @j2sNative
+ *
+ * if (newLength < oldLength) return Clazz.newArray(-1, array, 0,
newLength);
+ */
+ {}
short[] t = new short[newLength];
if (array != null) {
- int oldLength = array.length;
System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
: newLength);
}
@@ -291,11 +320,16 @@
}
public static byte[] arrayCopyByte(byte[] array, int newLength) {
- if (newLength < 0)
- newLength = array.length;
+ int oldLength = (array == null ? -1 : array.length);
+ if (newLength < 0) newLength = oldLength;
+ /**
+ * @j2sNative
+ *
+ * if (newLength < oldLength) return Clazz.newArray(-1, array, 0,
newLength);
+ */
+ {}
byte[] t = new byte[newLength];
if (array != null) {
- int oldLength = array.length;
System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
: newLength);
}
@@ -303,11 +337,16 @@
}
public static boolean[] arrayCopyBool(boolean[] array, int newLength) {
- if (newLength < 0)
- newLength = array.length;
+ int oldLength = (array == null ? -1 : array.length);
+ if (newLength < 0) newLength = oldLength;
+ /**
+ * @j2sNative
+ *
+ * if (newLength < oldLength) return Clazz.newArray(-1, array, 0,
newLength);
+ */
+ {}
boolean[] t = new boolean[newLength];
if (array != null) {
- int oldLength = array.length;
System.arraycopy(array, 0, t, 0, oldLength < newLength ? oldLength
: newLength);
}
@@ -584,7 +623,7 @@
public static boolean isAB(Object x) {
/**
* @j2sNative
- * return Clazz.isAI(x);
+ * return Clazz.isAB(x);
*/
{
return x instanceof byte[];
@@ -636,6 +675,7 @@
* process, but particularly out of file reading.
*
* @param b
+ * @return b
*/
public static byte[] ensureSignedBytes(byte[] b) {
if (b != null) {
Modified: branches/v14_4/Jmol/src/javajs/util/BS.java
===================================================================
--- branches/v14_4/Jmol/src/javajs/util/BS.java 2015-12-17 22:22:22 UTC (rev
20894)
+++ branches/v14_4/Jmol/src/javajs/util/BS.java 2015-12-20 22:01:37 UTC (rev
20895)
@@ -728,9 +728,18 @@
* @param n
*/
private void setLength(int n) {
+ /**
+ * @j2sNative
+ * if (n == this.words.length) return;
+ * if (n == this.wordsInUse) {
+ * this.words = Clazz.newArray(-1, this.words, 0, n);
+ * return;
+ * }
+ */
+ {}
int[] a = new int[n];
- System.arraycopy(words, 0, a, 0, Math.min(wordsInUse, n));
- words = a;
+ System.arraycopy(words, 0, a, 0, wordsInUse);
+ words = a;
}
/**
@@ -798,8 +807,21 @@
if (wordCount == 0) {
bs.words = emptyBitmap;
} else {
- bs.words = new int[bs.wordsInUse = wordCount];
- System.arraycopy(bitsetToCopy.words, 0, bs.words, 0, wordCount);
+
+ /**
+ * Clazz.clone will copy wordsInUse and sizeIsSticky,
+ * but just a pointer to the words array.
+ *
+ * @j2sNative
+ *
+ * bs.words = Clazz.newArray(-1, bitsetToCopy.words, 0, bs.wordsInUse
= wordCount);
+ *
+ */
+ {
+ bs.words = new int[bs.wordsInUse = wordCount];
+ System.arraycopy(bitsetToCopy.words, 0, bs.words, 0, wordCount);
+ }
+
}
return bs;
}
@@ -820,8 +842,8 @@
@Override
public String toJSON() {
- int numBits = (wordsInUse > 128) ? cardinality() : wordsInUse
- * BITS_PER_WORD;
+ int numBits = (wordsInUse > 128 ? cardinality() : wordsInUse
+ * BITS_PER_WORD);
SB b = SB.newN(6 * numBits + 2);
b.appendC('[');
Modified: branches/v14_4/Jmol/src/javajs/util/CompoundDocHeader.java
===================================================================
--- branches/v14_4/Jmol/src/javajs/util/CompoundDocHeader.java 2015-12-17
22:22:22 UTC (rev 20894)
+++ branches/v14_4/Jmol/src/javajs/util/CompoundDocHeader.java 2015-12-20
22:01:37 UTC (rev 20895)
@@ -77,10 +77,10 @@
final boolean readData() {
try {
cd.readByteArray(magicNumbers, 0, 8);
- if (magicNumbers[0] != (byte) 0xD0 || magicNumbers[1] != (byte) 0xCF
- || magicNumbers[2] != (byte) 0x11 || magicNumbers[3] != (byte) 0xE0
- || magicNumbers[4] != (byte) 0xA1 || magicNumbers[5] != (byte) 0xB1
- || magicNumbers[6] != (byte) 0x1A || magicNumbers[7] != (byte) 0xE1)
+ if ((magicNumbers[0] & 0xFF) != 0xD0 || (magicNumbers[1] & 0xFF) != 0xCF
+ || (magicNumbers[2] & 0xFF) != 0x11 || (magicNumbers[3] & 0xFF) !=
0xE0
+ || (magicNumbers[4] & 0xFF) != 0xA1 || (magicNumbers[5] & 0xFF) !=
0xB1
+ || (magicNumbers[6] & 0xFF) != 0x1A || (magicNumbers[7] & 0xFF) !=
0xE1)
return false;
cd.readByteArray(uniqueID16, 0, 16);
revNumber = cd.readByte();
Modified: branches/v14_4/Jmol/src/javajs/util/PT.java
===================================================================
--- branches/v14_4/Jmol/src/javajs/util/PT.java 2015-12-17 22:22:22 UTC (rev
20894)
+++ branches/v14_4/Jmol/src/javajs/util/PT.java 2015-12-20 22:01:37 UTC (rev
20895)
@@ -863,7 +863,7 @@
}
/**
- * Checks to see if an object is an array, and if it is, returns null;
+ * Checks to see if an object is an array (including typed arrays), and if
it is, returns null;
* otherwise it returns the string equivalent of that object.
*
* @param x
@@ -873,7 +873,7 @@
/**
* @j2sNative
*
- * return (x.constructor == Array ? null : x.toString());
+ * return (x.constructor == Array || x.BYTES_PER_ELEMENT ? null :
x.toString());
*
*/
{
Modified: branches/v14_4/Jmol/src/javajs/util/Rdr.java
===================================================================
--- branches/v14_4/Jmol/src/javajs/util/Rdr.java 2015-12-17 22:22:22 UTC
(rev 20894)
+++ branches/v14_4/Jmol/src/javajs/util/Rdr.java 2015-12-20 22:01:37 UTC
(rev 20895)
@@ -96,17 +96,17 @@
}
private static Encoding getUTFEncoding(byte[] bytes) {
- if (bytes.length >= 3 && bytes[0] == (byte) 0xEF && bytes[1] == (byte)
0xBB && bytes[2] == (byte) 0xBF)
+ if (bytes.length >= 3 && (bytes[0] & 0xFF) == 0xEF && (bytes[1] & 0xFF) ==
0xBB && (bytes[2] & 0xFF) == 0xBF)
return Encoding.UTF8;
- if (bytes.length >= 4 && bytes[0] == (byte) 0 && bytes[1] == (byte) 0
- && bytes[2] == (byte) 0xFE && bytes[3] == (byte) 0xFF)
+ if (bytes.length >= 4 && (bytes[0] & 0xFF) == 0 && (bytes[1] & 0xFF) == 0
+ && (bytes[2] & 0xFF) == 0xFE && (bytes[3] & 0xFF) == 0xFF)
return Encoding.UTF_32BE;
- if (bytes.length >= 4 && bytes[0] == (byte) 0xFF && bytes[1] == (byte)
0xFE
- && bytes[2] == (byte) 0 && bytes[3] == (byte) 0)
+ if (bytes.length >= 4 && (bytes[0] & 0xFF) == 0xFF && (bytes[1] & 0xFF) ==
0xFE
+ && (bytes[2] & 0xFF) == 0 && (bytes[3] & 0xFF) == 0)
return Encoding.UTF_32LE;
- if (bytes.length >= 2 && bytes[0] == (byte) 0xFF && bytes[1] == (byte)
0xFE)
+ if (bytes.length >= 2 && (bytes[0] & 0xFF) == 0xFF && (bytes[1] & 0xFF) ==
0xFE)
return Encoding.UTF_16LE;
- if (bytes.length >= 2 && bytes[0] == (byte) 0xFE && bytes[1] == (byte)
0xFF)
+ if (bytes.length >= 2 && (bytes[0] & 0xFF) == 0xFE && (bytes[1] & 0xFF) ==
0xFF)
return Encoding.UTF_16BE;
return Encoding.NONE;
@@ -145,11 +145,11 @@
}
public static boolean isCompoundDocumentB(byte[] bytes) {
- return (bytes.length >= 8 && bytes[0] == (byte) 0xD0
- && bytes[1] == (byte) 0xCF && bytes[2] == (byte) 0x11
- && bytes[3] == (byte) 0xE0 && bytes[4] == (byte) 0xA1
- && bytes[5] == (byte) 0xB1 && bytes[6] == (byte) 0x1A
- && bytes[7] == (byte) 0xE1);
+ return (bytes.length >= 8 && (bytes[0] & 0xFF) == 0xD0
+ && (bytes[1] & 0xFF) == 0xCF && (bytes[2] & 0xFF) == 0x11
+ && (bytes[3] & 0xFF) == 0xE0 && (bytes[4] & 0xFF) == 0xA1
+ && (bytes[5] & 0xFF) == 0xB1 && (bytes[6] & 0xFF) == 0x1A
+ && (bytes[7] & 0xFF) == 0xE1);
}
public static boolean isGzipS(InputStream is) {
@@ -158,7 +158,7 @@
public static boolean isGzipB(byte[] bytes) {
return (bytes != null && bytes.length >= 2
- && bytes[0] == (byte) 0x1F && bytes[1] == (byte) 0x8B);
+ && (bytes[0] & 0xFF) == 0x1F && (bytes[1] & 0xFF) == 0x8B);
}
public static boolean isPickleS(InputStream is) {
@@ -167,7 +167,7 @@
public static boolean isPickleB(byte[] bytes) {
return (bytes != null && bytes.length >= 2
- && bytes[0] == (byte) 0x7D && bytes[1] == (byte) 0x71);
+ && (bytes[0] & 0xFF) == 0x7D && (bytes[1] & 0xFF) == 0x71);
}
public static boolean isPngZipStream(InputStream is) {
Modified: branches/v14_4/Jmol/src/org/jmol/applet/Jmol.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/applet/Jmol.java 2015-12-17 22:22:22 UTC
(rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/applet/Jmol.java 2015-12-20 22:01:37 UTC
(rev 20895)
@@ -24,26 +24,26 @@
package org.jmol.applet;
-import org.jmol.awt.FileDropper;
-import org.jmol.c.CBK;
-import org.jmol.util.GenericApplet;
-import org.jmol.util.Logger;
-import org.jmol.util.Parser;
-
import java.applet.Applet;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Graphics;
import java.net.URL;
-import javajs.util.PT;
-
import java.util.Hashtable;
import java.util.Map;
+import javajs.util.PT;
+
import javax.swing.UIManager;
import netscape.javascript.JSObject;
+import org.jmol.awt.FileDropper;
+import org.jmol.c.CBK;
+import org.jmol.util.GenericApplet;
+import org.jmol.util.Logger;
+import org.jmol.util.Parser;
+
/*
*
*
Modified: branches/v14_4/Jmol/src/org/jmol/appletjs/Jmol.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/appletjs/Jmol.java 2015-12-17 22:22:22 UTC
(rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/appletjs/Jmol.java 2015-12-20 22:01:37 UTC
(rev 20895)
@@ -24,22 +24,21 @@
package org.jmol.appletjs;
-import org.jmol.util.Logger;
-import org.jmol.util.Parser;
-import org.jmol.util.GenericApplet;
-
import java.net.URL;
+import java.util.Hashtable;
+import java.util.Map;
import javajs.api.JSInterface;
import javajs.util.PT;
-import java.util.Hashtable;
-import java.util.Map;
+import org.jmol.util.GenericApplet;
+import org.jmol.util.Logger;
+import org.jmol.util.Parser;
/**
* Java2Script rendition of Jmol using HTML5-only or WebGL-based graphics
*
- * @author Bob Hanson hans...@stolaf.edu, Takanori Nakane, with the assistance
+ * @author Bob Hanson hans...@stolaf.edu, Takanori Nakane, with the assistance
* of Jhou Renjian
*
*/
@@ -128,7 +127,7 @@
/**
* @j2sNative
*
- * fxy[i][j] = eval(functionName)(this.htmlName, i, j);
+ * fxy[i][j] = window.eval(functionName)(this.htmlName,
i, j);
*/
{
}
@@ -138,7 +137,7 @@
/**
* @j2sNative
*
- * data = eval(functionName)(this.htmlName, nX, nY);
+ * data = window.eval(functionName)(this.htmlName, nX, nY);
*
*/
{
@@ -156,7 +155,7 @@
/**
* @j2sNative
*
- * data = eval(functionName)(this.htmlName, nX, nY, fxy);
+ * data = window.eval(functionName)(this.htmlName, nX, nY,
fxy);
*
*/
{
@@ -182,7 +181,7 @@
/**
* @j2sNative
*
- * eval(functionName)(this.htmlName, nX, nY, nZ, fxyz);
+ * window.eval(functionName)(this.htmlName, nX, nY, nZ, fxyz);
*
*/
{
@@ -240,13 +239,17 @@
return "";
}
+ /**
+ * return RAW JAVASCRIPT OBJECT, NOT A STRING
+ */
@Override
protected String doEval(String strEval) {
try {
/**
+ *
* @j2sNative
*
- * return "" + eval(strEval);
+ * return window.eval(strEval);
*/
{
}
Modified: branches/v14_4/Jmol/src/org/jmol/jvxl/readers/IsoFxyReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/jvxl/readers/IsoFxyReader.java
2015-12-17 22:22:22 UTC (rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/jvxl/readers/IsoFxyReader.java
2015-12-20 22:01:37 UTC (rev 20895)
@@ -99,7 +99,7 @@
@Override
public float[] getPlane(int x) {
- float[] plane = getPlane2(x);
+ float[] plane = getPlaneSR(x);
setPlane(x, plane);
return plane;
}
Modified: branches/v14_4/Jmol/src/org/jmol/jvxl/readers/IsoMOReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/jvxl/readers/IsoMOReader.java
2015-12-17 22:22:22 UTC (rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/jvxl/readers/IsoMOReader.java
2015-12-20 22:01:37 UTC (rev 20895)
@@ -343,7 +343,7 @@
public float[] getPlane(int x) {
if (!qSetupDone)
setupCalculation();
- return getPlane2(x);
+ return getPlaneSR(x);
}
private boolean qSetupDone;
Modified: branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
2015-12-17 22:22:22 UTC (rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
2015-12-20 22:01:37 UTC (rev 20895)
@@ -547,10 +547,10 @@
@Override
public float[] getPlane(int x) {
- return getPlane2(x);
+ return getPlaneSR(x);
}
- protected float[] getPlane2(int x) {
+ protected float[] getPlaneSR(int x) {
if (yzCount == 0)
initPlanes();
if (qpc != null)
Modified: branches/v14_4/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java
2015-12-17 22:22:22 UTC (rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java
2015-12-20 22:01:37 UTC (rev 20895)
@@ -327,9 +327,9 @@
initPlanes();
if (preProcessPlanes)
return getPlaneProcessed(x);
- float[] plane = getPlane2(x);
+ float[] plane = getPlaneSR(x);
if (qpc == null)
- getPlane(plane, true);
+ getPlaneVFR(plane, true);
return plane;
}
@@ -362,8 +362,8 @@
qpc.setPlanes(yzPlanesRaw = new float[4][yzCount]);
if (hasColorData) {
//float nan = qpc.getNoValue();
- getPlane(yzPlanesRaw[0], false);
- getPlane(yzPlanesRaw[1], false);
+ getPlaneVFR(yzPlanesRaw[0], false);
+ getPlaneVFR(yzPlanesRaw[1], false);
plane = yzPlanes[0];
for (int i = 0; i < yzCount; i++)
plane[i] = Float.NaN;
@@ -391,7 +391,7 @@
plane = yzPlanesRaw[iPlaneRaw];
}
if (x < x1) {
- getPlane(plane, false);
+ getPlaneVFR(plane, false);
qpc.calcPlane(x, plane = yzPlanes[x % 2]);
for (int i = 0; i < yzCount; i++)
if (plane[i] != nan)
@@ -403,7 +403,7 @@
return plane;
}
- private void getPlane(float[] plane, boolean doRecord) {
+ private void getPlaneVFR(float[] plane, boolean doRecord) {
try {
for (int y = 0, ptyz = 0; y < nPointsY; ++y) {
for (int z = 0; z < nPointsZ; ++z) {
Modified: branches/v14_4/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/modelset/Atom.java 2015-12-17 22:22:22 UTC
(rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/modelset/Atom.java 2015-12-20 22:01:37 UTC
(rev 20895)
@@ -441,7 +441,7 @@
public void setValence(int nBonds) {
if (!isDeleted()) // no resurrection
- valence = (byte) (nBonds < 0 ? 0 : nBonds < 0xEF ? nBonds : 0xEF);
+ valence = (byte) (nBonds < 0 ? 0 : nBonds <= 0x7F ? nBonds : 0x7F);
}
/**
Modified: branches/v14_4/Jmol/src/org/jmol/script/SV.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/SV.java 2015-12-17 22:22:22 UTC
(rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/script/SV.java 2015-12-20 22:01:37 UTC
(rev 20895)
@@ -86,6 +86,13 @@
return sv;
}
+ public static SV newF(float f) {
+ SV sv = new SV();
+ sv.tok = decimal;
+ sv.value = Float.valueOf(f);
+ return sv;
+ }
+
public static SV newS(String s) {
return newV(string, s);
}
@@ -267,6 +274,7 @@
if (x instanceof ScriptContext)
return newV(context, x);
// rest are specific array types supported
+ // DO NOT ADD MORE UNLESS YOU CHANGE isArray(), above
if (Escape.isAV(x))
return getVariableAV((SV[]) x);
if (AU.isAI(x))
@@ -291,12 +299,53 @@
return getVariableADD((double[][]) x);
if (AU.isAFloat(x))
return newV(listf, x);
- return newS(x.toString());
+ return newJSVar(x);
}
+ /**
+ * Conversion to Jmol variables of JavaScript variables using
+ * y = javascript("x")
+ *
+ * @param x a JavaScript variable, perhaps
+ * @return SV
+ */
+ @SuppressWarnings("unused")
+ private static SV newJSVar(Object x) {
+ // JavaScript only
+ /**
+ * @j2sNative
+ *
+ * switch(x.BYTES_PER_ELEMENT ? Array : x.constructor) {
+ * case Boolean:
+ * return (x ? org.jmol.script.SV.vT : org.jmol.script.SV.vF);
+ * case Number:
+ * return (x > Integer.MAX_VALUE || x != Math.floor(x) ?
org.jmol.script.SV.newF(x) : org.jmol.script.SV.newI(x));
+ * case Array:
+ * var v = new javajs.util.Lst();
+ * for (var i = 0, n = x.length; i < n; i++)
+ * v.addLast(org.jmol.script.SV.newJSVar(x[i]));
+ * return org.jmol.script.SV.getVariableList(v);
+ * case Object:
+ * var keys = Object.keys(x);
+ * var v = new java.util.Hashtable();
+ * for (var i = keys.length; --i >= 0;)
+ * v.put(keys[i],org.jmol.script.SV.newJSVar(x[keys[i]]));
+ * return org.jmol.script.SV.getVariableMap(v);
+ * }
+ *
+ */
+ {
+ // for reference only; not included in JavaScript
+ if (false) {
+ getVariableList(new Lst<SV>());
+ getVariableMap(new Hashtable<String, Object>());
+ }
+ }
+ return newS(x.toString());
+ }
+
@SuppressWarnings("unchecked")
- public
- static SV getVariableMap(Map<String, ?> x) {
+ public static SV getVariableMap(Map<String, ?> x) {
Map<String, Object> ht = (Map<String, Object>) x;
Object o = null;
for (Object oo : ht.values()) {
@@ -1080,16 +1129,17 @@
intValue = index = Integer.MAX_VALUE;
break;
case varray:
- len = getList().size();
+ @SuppressWarnings("unchecked")
+ Lst<SV> v = (Lst<SV>) value;
+ len = v.size();
if (pt1 <= 0)
pt1 = len + pt1;
if (--pt1 < 0)
pt1 = 0;
- if (len <= pt1) {
+ if (len <= pt1)
for (int i = len; i <= pt1; i++)
- getList().addLast(newV(string, ""));
- }
- getList().set(pt1, var);
+ v.addLast(newV(string, ""));
+ v.set(pt1, var);
break;
}
}
@@ -1217,12 +1267,13 @@
.indexOf(";" + format.toLowerCase() + ";"));
}
- /**
- * Accepts arguments from the format() function First argument is a
- * format string.
+ /**
+ * Accepts arguments from the format() function First argument is a format
+ * string.
*
* @param args
- * @param pt 0: to JSON, 5: to base64, 12: to bytearray, 22: to array
+ * @param pt
+ * 0: to JSON, 5: to base64, 12: to bytearray, 22: to array
* @return formatted string
*/
public static Object format(SV[] args, int pt) {
@@ -1263,7 +1314,7 @@
break;
default:
String s = args[1].asString();
- if (s.startsWith(";base64,")){
+ if (s.startsWith(";base64,")) {
if (pt == 5)
return s;
bytes = Base64.decodeBase64(s);
@@ -1271,8 +1322,8 @@
bytes = s.getBytes();
}
}
- return (pt == 22 ? getVariable(bytes) : pt == 12 ? new BArray(bytes) :
";base64,"
- + javajs.util.Base64.getBase64(bytes).toString());
+ return (pt == 22 ? getVariable(bytes) : pt == 12 ? new BArray(bytes)
+ : ";base64," + javajs.util.Base64.getBase64(bytes).toString());
}
}
// use values to replace codes in format string
@@ -1283,9 +1334,8 @@
sb.append(format[0]);
for (int i = 1; i < format.length; i++) {
Object ret = sprintf(PT.formatCheck("%" + format[i]),
- (args[1].tok == hash ? args[1]
- : args[1].tok == varray ? args[1].getList().get(i - 1)
- : i < args.length ? args[i] : null));
+ (args[1].tok == hash ? args[1] : args[1].tok == varray ? args[1]
+ .getList().get(i - 1) : i < args.length ? args[i] : null));
if (AU.isAS(ret)) {
String[] list = (String[]) ret;
for (int j = 0; j < list.length; j++)
@@ -1450,12 +1500,23 @@
* @return array
*/
public SV pushPop(SV value, SV mapKey) {
- if (mapKey != null ) {
+ if (mapKey != null) {
Map<String, SV> m = getMap();
if (value == null) {
- SV v;
- return (m == null || (v = m.remove(mapKey.asString())) == null ?
- newS("") : v);
+ SV v = null;
+ if (m == null) {
+ Lst<SV> lst = getList();
+ int len = lst.size();
+ int i = iValue(mapKey) - 1;
+ if (i < 0)
+ i += len;
+ if (i >= 0 && i < len) {
+ v = lst.remove(i);
+ }
+ } else {
+ v = m.remove(mapKey.asString());
+ }
+ return (v == null ? newS("") : v);
}
if (m != null)
m.put(mapKey.asString(), newI(0).setv(value));
@@ -1500,27 +1561,6 @@
return list;
}
-// I have no idea!
-//
-// static List<Object> listAny(SV x) {
-// List<Object> list = new List<Object>();
-// List<SV> l = x.getList();
-// for (int i = 0; i < l.size(); i++) {
-// SV v = l.get(i);
-// List<SV> l2 = v.getList();
-// if (l2 == null) {
-// list.addLast(v.value);
-// } else {
-// List<Object> o = new List<Object>();
-// for (int j = 0; j < l2.size(); j++) {
-// v = l2.get(j);
-// }
-// list.addLast(o);
-// }
-// }
-// return list;
-// }
-
public static float[] flistValue(T x, int nMin) {
if (x.tok != varray)
return new float[] { fValue(x) };
@@ -1765,4 +1805,5 @@
+ (property instanceof SV ? PT.esc(key) + " : " + format(new SV[] {
null, (SV) property },
0) : PT.toJSON(key, property)) + "}";
}
+
}
Modified: branches/v14_4/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2015-12-17 22:22:22 UTC (rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/script/ScriptMathProcessor.java
2015-12-20 22:01:37 UTC (rev 20895)
@@ -274,7 +274,7 @@
public boolean addXFloat(float x) {
if (Float.isNaN(x))
return addXStr("NaN");
- putX(SV.newV(T.decimal, Float.valueOf(x)));
+ putX(SV.newF(x));
return wasX = true;
}
@@ -309,7 +309,7 @@
float f = ((Float) x.value).floatValue();
if (f < 0 || f == 0 && 1 / f == Float.NEGATIVE_INFINITY) {
addOp(T.tokenMinus);
- v = SV.newV(T.decimal, Float.valueOf(-f));
+ v = SV.newF(-f);
break;
}
}
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-12-17
22:22:22 UTC (rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-12-20
22:01:37 UTC (rev 20895)
@@ -1131,6 +1131,7 @@
boolean isPmesh = (iShape == JC.SHAPE_PMESH);
boolean isPlot3d = (iShape == JC.SHAPE_PLOT3D);
boolean isLcaoCartoon = (iShape == JC.SHAPE_LCAOCARTOON);
+ boolean isSilent = (isLcaoCartoon || tokAt(1) == T.delete);
boolean surfaceObjectSeen = false;
boolean planeSeen = false;
boolean isMapped = false;
@@ -1191,6 +1192,10 @@
str = paramAsStr(i);
switch (eval.theTok) {
// settings only
+ case T.silent:
+ isSilent = true;
+ sbCommand.append(" silent");
+ continue;
case T.isosurfacepropertysmoothing:
smoothing = (getToken(++i).tok == T.on ? Boolean.TRUE
: eval.theTok == T.off ? Boolean.FALSE : null);
@@ -2738,7 +2743,7 @@
+ Escape.eBS(bsSelect) + " ")
+ cmd);
s = (String) getShapeProperty(iShape, "ID");
- if (s != null && !eval.tQuiet) {
+ if (s != null && !eval.tQuiet && !isSilent) {
cutoff = ((Float) getShapeProperty(iShape, "cutoff")).floatValue();
if (Float.isNaN(cutoff) && !Float.isNaN(sigma))
Logger.error("sigma not supported");
@@ -2765,7 +2770,7 @@
s += "\n" + svol;
}
}
- if (s != null)
+ if (s != null && !isSilent)
showString(s);
}
if (translucency != null)
@@ -2773,7 +2778,7 @@
setShapeProperty(iShape, "clear", null);
if (toCache)
setShapeProperty(iShape, "cache", null);
- if (iShape != JC.SHAPE_LCAOCARTOON && !isDisplay && !haveSlab)
+ if (!isSilent && !isDisplay && !haveSlab && eval.theTok != T.delete)
listIsosurface(iShape);
}
@@ -3540,7 +3545,7 @@
+ ret + "}", false);
Lst<SV> params = new Lst<SV>();
for (int i = 0; i < xyz.length(); i += 2)
- params.addLast(SV.newV(T.decimal, Float.valueOf(0f)).setName(
+ params.addLast(SV.newF(0).setName(
xyz.substring(i, i + 1)));
return new Object[] { e.aatoken[0][1].value, params };
} catch (Exception ex) {
Modified: branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java 2015-12-17
22:22:22 UTC (rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/scriptext/MathExt.java 2015-12-20
22:01:37 UTC (rev 20895)
@@ -389,8 +389,8 @@
map.put("_bin", SV.newI(bin));
float v1 = f0 + df * bin;
float v2 = v1 + df;
- map.put("_binMin", SV.newV(T.decimal, Float.valueOf(bin == 0 ?
-Float.MAX_VALUE : v1)));
- map.put("_binMax", SV.newV(T.decimal, Float.valueOf(bin == nbins - 1
? Float.MAX_VALUE : v2)));
+ map.put("_binMin", SV.newF(bin == 0 ? -Float.MAX_VALUE : v1));
+ map.put("_binMax", SV.newF(bin == nbins - 1 ? Float.MAX_VALUE : v2));
}
}
return mp.addXAI(array);
@@ -726,9 +726,8 @@
*
*
*/
-
- boolean isBondCount = (tok == T.bondcount);
- if (args.length > 5 || isBondCount && args.length != 1)
+
+ if (args.length > 5)
return false;
float min = Integer.MIN_VALUE, max = Integer.MAX_VALUE;
float fmin = 0, fmax = Float.MAX_VALUE;
@@ -740,6 +739,9 @@
boolean isBonds = false;
switch (tok) {
case T.polyhedra:
+ // polyhedra()
+ // polyhedra(3)
+ // polyhedra(smilesString)
int nv = Integer.MIN_VALUE;
String smiles = null;
if (args.length > 0) {
@@ -756,6 +758,7 @@
vwr.shm.getShapePropertyData(JC.SHAPE_POLYHEDRA, "centers", data);
return mp.addXBs(data[2] == null ? new BS() : (BS) data[2]);
case T.bondcount:
+ // {atoms1}.bondCount({atoms2})
SV x1 = mp.getX();
if (x1.tok != T.bitset || args.length != 1 || args[0].tok != T.bitset)
return false;
@@ -773,6 +776,8 @@
}
return mp.addXList(list);
}
+
+ // connected(
for (int i = 0; i < args.length; i++) {
SV var = args[i];
switch (var.tok) {
@@ -1434,7 +1439,7 @@
*
* @param mp
* @param args
- * @param tok0
+ * @param tok0
* @param isAtomProperty
* @return true if no syntax problems
* @throws ScriptException
@@ -1451,7 +1456,9 @@
return mp.addXObj(vwr.extractProperty(args[0].value,
args[1].value.toString(), -1));
}
- String propertyName = (args.length > 0 ? SV.sValue(args[pt++]) : "");
+ BS bsSelect = (isAtomProperty && args.length == 1 && args[0].tok ==
T.bitset ? (BS) args[0].value : null);
+ String pname = (bsSelect == null && args.length > 0 ?
SV.sValue(args[pt++]) : "");
+ String propertyName = pname;
String lc = propertyName.toLowerCase();
if (!isSelect && lc.indexOf("[select ") < 0)
propertyName = lc;
@@ -1463,9 +1470,48 @@
SV x = null;
if (isAtomProperty) {
x = mp.getX();
- if (x.tok != T.bitset) {
+ switch (x.tok) {
+ case T.bitset:
+ break;
+ case T.string:
+ String name = (String) x.value;
+ Object[] data = new Object[3];
+ int shapeID;
+ if (name.startsWith("$")) {
+ // "$P4".getProperty....
+ name = name.substring(1);
+ shapeID = vwr.shm.getShapeIdFromObjectName(name);
+ if (shapeID >= 0) {
+ data[0] = name;
+ vwr.shm.getShapePropertyData(shapeID, "index", data);
+ if (data[1] != null && !pname.equals("index")) {
+ int index = ((Integer) data[1]).intValue();
+ data[1] = vwr.shm.getShapePropertyIndex(shapeID,
+ pname.intern(), index);
+ }
+ }
+ } else {
+ shapeID = JC.shapeTokenIndex(T.getTokFromName(name));
+ if (shapeID >= 0) {
+ // "isosurface".getProperty...
+ data[0] = pname;
+ data[1] = Integer.valueOf(-1);
+ vwr.shm.getShapePropertyData(shapeID, pname.intern(), data);
+ }
+ }
+ return (data[1] == null ? mp.addXStr("") : mp.addXObj(data[1]));
+ case T.varray:
+ if (bsSelect != null) {
+ Lst<SV> l0 = x.getList();
+ Lst<SV> lst = new Lst<SV>();
+ for (int i = bsSelect.nextSetBit(0); i >= 0; i =
bsSelect.nextSetBit(i + 1))
+ lst.addLast(l0.get(i));
+ return mp.addXList(lst);
+ }
+ //$FALL-THROUGH$
+ default:
if (isSelect)
- propertyName = "[SELECT " + propertyName + "]";
+ propertyName = "[SELECT " + propertyName + "]";
return mp.addXObj(vwr.extractProperty(x, propertyName, -1));
}
}
@@ -1828,14 +1874,14 @@
else if (Float.isNaN(list2[i]))
b = SV.getVariable(SV.unescapePointOrBitsetAsVariable(sList2[i]));
else
- b = SV.newV(T.decimal, Float.valueOf(list2[i]));
+ b = SV.newF(list2[i]);
if (!isScalar1) {
if (isArray1)
a = alist1.get(i);
else if (Float.isNaN(list1[i]))
a = SV.getVariable(SV.unescapePointOrBitsetAsVariable(sList1[i]));
else
- a = SV.newV(T.decimal, Float.valueOf(list1[i]));
+ a = SV.newF(list1[i]);
}
if (tok == T.join) {
if (a.tok != T.varray) {
@@ -2289,7 +2335,7 @@
}
if (args[1].tok == T.on) {
// this is TO screen coordinates, 0 at bottom left
- vwr.tm.transformPt3f(pt3, pt3);
+ vwr.tm.transformPt3f(pt3, pt3);
pt3.y = vwr.tm.height - pt3.y;
if (vwr.antialiased)
pt3.scale(0.5f);
@@ -2675,8 +2721,7 @@
e.runScriptBuffer("show " + s, sb, true);
break;
case T.javascript:
- sb.append(vwr.jsEval(s));
- break;
+ return mp.addX(vwr.jsEvalSV(s));
}
s = sb.toString();
float f;
@@ -3157,20 +3202,67 @@
if (pt != null) {
if (args[last].tok == T.varray) {
// within(dist, pt, [pt1, pt2, pt3...])
- Lst<SV> sv = args[2].getList();
+ Lst<SV> sv = args[last].getList();
Lst<T3> pts = new Lst<T3>();
Bspt bspt = new Bspt(3, 0);
- for (int i = sv.size(); --i >= 0;) {
+ CubeIterator iter;
+ if (Float.isNaN(pt.x)) {
+ // internal comparison
+ Point3fi p;
+ Point3fi[] pt3 = new Point3fi[sv.size()];
+ for (int i = pt3.length; --i >= 0;) {
+ P3 p3 = SV.ptValue(sv.get(i));
+ if (p3 == null)
+ return false;
+ p = new Point3fi();
+ p.setT(p3);
+ p.i = i;
+ pt3[i] = p;
+ bspt.addTuple(p);
+ }
+ iter = bspt.allocateCubeIterator();
+ BS bsp = BSUtil.newBitSet2(0, sv.size());
+ for (int i = pt3.length; --i >= 0;) {
+ iter.initialize(p = pt3[i], distance, false);
+ float d2 = distance * distance;
+ int n = 0;
+ while (iter.hasMoreElements()) {
+ Point3fi pt2 = (Point3fi) iter.nextElement();
+ if (bsp.get(pt2.i) && pt2.distanceSquared(p) <= d2 && (++n > 1))
+ bsp.clear(pt2.i);
+ }
+ }
+ for (int i = bsp.nextSetBit(0); i >= 0; i = bsp.nextSetBit(i + 1))
+ pts.addLast(P3.newP(pt3[i]));
+ return mp.addXList(pts);
+
+ }
+ float d2;
+ if (distance == 0) {
+ // closest
+ P3 pt3 = null, pta;
+ d2 = Float.MAX_VALUE;
+ for (int i = sv.size(); --i >= 0;) {
+ pta = SV.ptValue(sv.get(i));
+ distance = pta.distanceSquared(pt);
+ if (distance < d2) {
+ pt3 = pta;
+ d2 = distance;
+ }
+ }
+ return (pt3 == null ? mp.addXStr("") : mp.addXPt(pt3));
+ }
+ for (int i = sv.size(); --i >= 0;)
bspt.addTuple(SV.ptValue(sv.get(i)));
- }
- CubeIterator iter = bspt.allocateCubeIterator();
+ iter = bspt.allocateCubeIterator();
iter.initialize(pt, distance, false);
- float d2 = distance * distance;
+ d2 = distance * distance;
while (iter.hasMoreElements()) {
T3 pt2 = iter.nextElement();
if (pt2.distanceSquared(pt) <= d2)
pts.addLast(pt2);
}
+ iter.release();
return mp.addXList(pts);
}
return mp.addXBs(vwr.getAtomsNearPt(distance, pt));
Modified: branches/v14_4/Jmol/src/org/jmol/shape/AtomShape.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shape/AtomShape.java 2015-12-17
22:22:22 UTC (rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/shape/AtomShape.java 2015-12-20
22:01:37 UTC (rev 20895)
@@ -141,6 +141,8 @@
float[] sizes = (float[]) data[2];
RadiusData rd = new RadiusData(null, 0, RadiusData.EnumType.FACTOR,
VDW.AUTO);
+ if (bsColixSet == null)
+ bsColixSet = new BS();
if (bsSizeSet == null)
bsSizeSet = new BS();
int i0 = bs.nextSetBit(0);
@@ -205,9 +207,9 @@
if (colixes == null || n > colixes.length) {
colixes = AU.ensureLengthShort(colixes, n);
paletteIDs = AU.ensureLengthByte(paletteIDs, n);
- if (bsColixSet == null)
- bsColixSet = BS.newN(ac);
}
+ if (bsColixSet == null)
+ bsColixSet = BS.newN(ac);
return n;
}
Modified: branches/v14_4/Jmol/src/org/jmol/util/GenericApplet.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/util/GenericApplet.java 2015-12-17
22:22:22 UTC (rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/util/GenericApplet.java 2015-12-20
22:01:37 UTC (rev 20895)
@@ -6,7 +6,6 @@
import java.util.Hashtable;
import java.util.Map;
-import javajs.awt.Dimension;
import javajs.util.Lst;
import javajs.util.PT;
import javajs.util.SB;
@@ -73,7 +72,7 @@
abstract protected String getJmolParameter(String name);
// callback implementations
- abstract protected String doEval(String strEval);
+ abstract protected String doEval(String strEval); // in JavaScript, this
will be an Object, Number, String, etc.
abstract protected float[][] doFunctionXY(String functionName, int nX, int
nY);
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/AnimationManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/AnimationManager.java
2015-12-17 22:22:22 UTC (rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/AnimationManager.java
2015-12-20 22:01:37 UTC (rev 20895)
@@ -430,30 +430,41 @@
private int lastModelPainted;
private int intAnimThread;
public int cai = -1;
+
private void setViewer(boolean clearBackgroundModel) {
vwr.ms.setTrajectory(cmi);
vwr.tm.setFrameOffset(cmi);
if (cmi == -1 && clearBackgroundModel)
- setBackgroundModelIndex(-1);
+ setBackgroundModelIndex(-1);
vwr.setTainted(true);
- setFrameRangeVisible();
+ int nDisplay = setFrameRangeVisible();
vwr.setStatusFrameChanged(false, false);
- if (vwr.ms != null && !vwr.g.selectAllModels)
-
vwr.slm.setSelectionSubset(vwr.ms.getModelAtomBitSetIncludingDeleted(cmi,
true));
+ if (!vwr.g.selectAllModels)
+ setSelectAllSubset(nDisplay < 2);
}
- private void setFrameRangeVisible() {
+ void setSelectAllSubset(boolean justOne) {
+ if (vwr.ms != null)
+ vwr.slm.setSelectionSubset(justOne ? vwr.ms
+ .getModelAtomBitSetIncludingDeleted(cmi, true) : vwr.ms
+ .getModelAtomBitSetIncludingDeletedBs(bsVisibleModels));
+ }
+
+ private int setFrameRangeVisible() {
+ int nDisplayed = 0;
bsVisibleModels.clearAll();
- if (backgroundModelIndex >= 0)
+ if (backgroundModelIndex >= 0) {
bsVisibleModels.set(backgroundModelIndex);
+ nDisplayed = 1;
+ }
if (cmi >= 0) {
bsVisibleModels.set(cmi);
- return;
+ return ++nDisplayed;
}
if (frameStep == 0)
- return;
- int nDisplayed = 0;
+ return nDisplayed;
int frameDisplayed = 0;
+ nDisplayed = 0;
for (int iframe = firstFrameIndex; iframe != lastFrameIndex; iframe +=
frameStep) {
int i = modelIndexForFrame(iframe);
if (!vwr.ms.isJmolDataFrameForModel(i)) {
@@ -472,6 +483,7 @@
}
if (nDisplayed == 1 && cmi < 0)
setFrame(frameDisplayed);
+ return nDisplayed;
}
private void animation(boolean TF) {
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-17
22:22:22 UTC (rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-20
22:01:37 UTC (rev 20895)
@@ -7,9 +7,12 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.5.1_2015.12.16"
+Jmol.___JmolVersion="14.4.1_2015.12.20"
+code: (JavaScript) adding use of array.slice and implementing Java byte[] as
JavaScript Int8Array()
bug fix: array handling for labels very inefficient
+bug fix: y = javascript("x") only creates string equivalent of x, not actual
numerical/object values
+bug fix: y = javascript("x") draws "x" from wrapped anonymous function using
eval() instead of global context using window.eval()
JmolVersion="14.4.1_2015.12.15"
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/SelectionManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/SelectionManager.java
2015-12-17 22:22:22 UTC (rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/SelectionManager.java
2015-12-20 22:01:37 UTC (rev 20895)
@@ -89,11 +89,15 @@
}
void display(ModelSet modelSet, BS bs, int addRemove, boolean isQuiet) {
- BS bsNotSubset = (bsSubset == null ? null :
BSUtil.andNot(BSUtil.copy(bsHidden), bsSubset));
switch (addRemove) {
default:
+ BS bsNotSubset = (bsSubset == null ? null :
BSUtil.andNot(BSUtil.copy(bsHidden), bsSubset));
BS bsAll = modelSet.getModelAtomBitSetIncludingDeleted(-1, false);
bsHidden.or(bsAll);
+ if (bsNotSubset != null) {
+ bsHidden.and(bsSubset);
+ bsHidden.or(bsNotSubset);
+ }
//$FALL-THROUGH$
case T.add:
if (bs != null)
@@ -104,10 +108,6 @@
bsHidden.or(bs);
break;
}
- if (bsNotSubset != null) {
- bsHidden.and(bsSubset);
- bsHidden.or(bsNotSubset);
- }
BSUtil.andNot(bsHidden, bsDeleted);
modelSet.setBsHidden(bsHidden);
if (!isQuiet)
@@ -115,7 +115,7 @@
}
void hide(ModelSet modelSet, BS bs, int addRemove, boolean isQuiet) {
- BS bsNotSubset = (bsSubset == null ? null :
BSUtil.andNot(BSUtil.copy(bsHidden), bsSubset));
+ BS bsNotSubset = (addRemove == 0 || bsSubset == null ? null :
BSUtil.andNot(BSUtil.copy(bsHidden), bsSubset));
setBitSet(bsHidden, bs, addRemove);
if (bsNotSubset != null)
bsHidden.or(bsNotSubset);
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/StatusManager.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/StatusManager.java 2015-12-17
22:22:22 UTC (rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/StatusManager.java 2015-12-20
22:01:37 UTC (rev 20895)
@@ -692,6 +692,12 @@
jsl.functionXYZ(functionName, nX, nY, nZ));
}
+ /**
+ *
+ * @param strEval
+ * @return in Java a String; in JavaScript window.eval()
+ *
+ */
String jsEval(String strEval) {
return (jsl == null ? "" : jsl.eval(strEval));
}
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2015-12-17 22:22:22 UTC
(rev 20894)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Viewer.java 2015-12-20 22:01:37 UTC
(rev 20895)
@@ -265,7 +265,7 @@
String logFilePath = "";
private boolean allowScripting;
- public boolean isPrintOnly = false;
+ public boolean isPrintOnly;
public boolean isSignedApplet = false;
private boolean isSignedAppletLocal = false;
private boolean isSilent;
@@ -1781,18 +1781,19 @@
ligandModelSet.put(id, Boolean.TRUE);
if (ligandModels == null)
ligandModels = new Hashtable<String, Object>();
- boolean isPng = (id.indexOf("|") > 0);
- if (isPng)
+ int pngPt = id.indexOf("|");
+ if (pngPt >= 0)
id = id.substring(id.indexOf("|") + 1);
Object model = (terminator == null ? ligandModels.get(id) : null);
String data;
String fname = null;
if (model instanceof Boolean)
return null;
- if (model == null && (terminator == null || isPng))
+ if (model == null && (terminator == null || pngPt >= 0))
model = ligandModels.get(id + suffix);
boolean isError = false;
- if (model == null) {
+ boolean isNew = (model == null);
+ if (isNew) {
String s;
if (isLigand) {
fname = (String) setLoadFormat("#" + id, '#', false);
@@ -1801,6 +1802,7 @@
scriptEcho("fetching " + fname);
s = getFileAsString3(fname, false, null);
} else {
+ scriptEcho("fetching " + prefix);
s = getFileAsString3(prefix, false, null);
int pt = (terminator == null ? -1 : s.indexOf(terminator));
if (pt >= 0)
@@ -1811,8 +1813,11 @@
if (!isError)
ligandModels.put(id + suffix, model);
}
- if (!isLigand)
+ if (!isLigand) {
+ if (!isNew)
+ scriptEcho(prefix + " loaded from cache");
return model;
+ }
// process ligand business
if (!isError && model instanceof String) {
@@ -3725,6 +3730,7 @@
@Override
public String evalFile(String strFilename) {
+ // from JmolApp and test suite only
return (allowScripting && getScriptManager() != null ? scm
.evalFile(strFilename) : null);
}
@@ -4635,9 +4641,13 @@
*/
public String jsEval(String strEval) {
- return sm.jsEval(strEval);
+ return "" + sm.jsEval(strEval);
}
+ public SV jsEvalSV(String strEval) {
+ return SV.getVariable(isJS ? sm.jsEval(strEval) : jsEval(strEval));
+ }
+
/*
* loadStructCallback indicates file load status.
*
@@ -5740,7 +5750,7 @@
break;
default:
if (!g.htNonbooleanParameterValues.containsKey(key.toLowerCase())) {
- g.setUserVariable(key, SV.newV(T.decimal, Float.valueOf(value)));
+ g.setUserVariable(key, SV.newF(value));
return;
}
}
@@ -6214,7 +6224,7 @@
if (value)
slm.setSelectionSubset(null);
else
- slm.setSelectionSubset(ms.getModelAtomBitSetIncludingDeleted(am.cmi,
true));
+ am.setSelectAllSubset(false);
break;
case T.messagestylechime:
// 11.5.39
This was sent by the SourceForge.net collaborative development platform, the
world's largest Open Source development site.
------------------------------------------------------------------------------
_______________________________________________
Jmol-commits mailing list
Jmol-commits@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-commits
