Revision: 20896
http://sourceforge.net/p/jmol/code/20896
Author: hansonr
Date: 2015-12-20 22:03:44 +0000 (Sun, 20 Dec 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.5.1_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:
--------------
trunk/Jmol/src/javajs/util/AU.java
trunk/Jmol/src/javajs/util/BS.java
trunk/Jmol/src/javajs/util/CompoundDocHeader.java
trunk/Jmol/src/javajs/util/PT.java
trunk/Jmol/src/javajs/util/Rdr.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
trunk/Jmol/src/org/jmol/applet/Jmol.java
trunk/Jmol/src/org/jmol/appletjs/Jmol.java
trunk/Jmol/src/org/jmol/jvxl/readers/IsoFxyReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/IsoMOReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java
trunk/Jmol/src/org/jmol/modelset/Atom.java
trunk/Jmol/src/org/jmol/script/SV.java
trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/shape/AtomShape.java
trunk/Jmol/src/org/jmol/shape/Labels.java
trunk/Jmol/src/org/jmol/util/GenericApplet.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/StatusManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/javajs/util/AU.java
===================================================================
--- trunk/Jmol/src/javajs/util/AU.java 2015-12-20 22:01:37 UTC (rev 20895)
+++ trunk/Jmol/src/javajs/util/AU.java 2015-12-20 22:03:44 UTC (rev 20896)
@@ -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: trunk/Jmol/src/javajs/util/BS.java
===================================================================
--- trunk/Jmol/src/javajs/util/BS.java 2015-12-20 22:01:37 UTC (rev 20895)
+++ trunk/Jmol/src/javajs/util/BS.java 2015-12-20 22:03:44 UTC (rev 20896)
@@ -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: trunk/Jmol/src/javajs/util/CompoundDocHeader.java
===================================================================
--- trunk/Jmol/src/javajs/util/CompoundDocHeader.java 2015-12-20 22:01:37 UTC
(rev 20895)
+++ trunk/Jmol/src/javajs/util/CompoundDocHeader.java 2015-12-20 22:03:44 UTC
(rev 20896)
@@ -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: trunk/Jmol/src/javajs/util/PT.java
===================================================================
--- trunk/Jmol/src/javajs/util/PT.java 2015-12-20 22:01:37 UTC (rev 20895)
+++ trunk/Jmol/src/javajs/util/PT.java 2015-12-20 22:03:44 UTC (rev 20896)
@@ -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: trunk/Jmol/src/javajs/util/Rdr.java
===================================================================
--- trunk/Jmol/src/javajs/util/Rdr.java 2015-12-20 22:01:37 UTC (rev 20895)
+++ trunk/Jmol/src/javajs/util/Rdr.java 2015-12-20 22:03:44 UTC (rev 20896)
@@ -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: trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2015-12-20 22:01:37 UTC (rev 20895)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2015-12-20 22:03:44 UTC (rev 20896)
@@ -187,7 +187,7 @@
return;
case JC.SHAPE_LABELS:
sm.loadShape(id);
- sm.setShapePropertyBs(id, "textLabels", info, bsAtoms);
+ sm.setShapePropertyBs(id, "pymolLabels", info, bsAtoms);
return;
case T.bonds:
break;
Modified: trunk/Jmol/src/org/jmol/applet/Jmol.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/Jmol.java 2015-12-20 22:01:37 UTC (rev
20895)
+++ trunk/Jmol/src/org/jmol/applet/Jmol.java 2015-12-20 22:03:44 UTC (rev
20896)
@@ -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;
+
/*
*
*
@@ -679,5 +679,4 @@
//ignore if page is closing
}
}
-
}
Modified: trunk/Jmol/src/org/jmol/appletjs/Jmol.java
===================================================================
--- trunk/Jmol/src/org/jmol/appletjs/Jmol.java 2015-12-20 22:01:37 UTC (rev
20895)
+++ trunk/Jmol/src/org/jmol/appletjs/Jmol.java 2015-12-20 22:03:44 UTC (rev
20896)
@@ -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: trunk/Jmol/src/org/jmol/jvxl/readers/IsoFxyReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/IsoFxyReader.java 2015-12-20
22:01:37 UTC (rev 20895)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/IsoFxyReader.java 2015-12-20
22:03:44 UTC (rev 20896)
@@ -99,7 +99,7 @@
@Override
public float[] getPlane(int x) {
- float[] plane = getPlane2(x);
+ float[] plane = getPlaneSR(x);
setPlane(x, plane);
return plane;
}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/IsoMOReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/IsoMOReader.java 2015-12-20
22:01:37 UTC (rev 20895)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/IsoMOReader.java 2015-12-20
22:03:44 UTC (rev 20896)
@@ -343,7 +343,7 @@
public float[] getPlane(int x) {
if (!qSetupDone)
setupCalculation();
- return getPlane2(x);
+ return getPlaneSR(x);
}
private boolean qSetupDone;
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java 2015-12-20
22:01:37 UTC (rev 20895)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java 2015-12-20
22:03:44 UTC (rev 20896)
@@ -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: trunk/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java 2015-12-20
22:01:37 UTC (rev 20895)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/VolumeFileReader.java 2015-12-20
22:03:44 UTC (rev 20896)
@@ -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: trunk/Jmol/src/org/jmol/modelset/Atom.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/Atom.java 2015-12-20 22:01:37 UTC (rev
20895)
+++ trunk/Jmol/src/org/jmol/modelset/Atom.java 2015-12-20 22:03:44 UTC (rev
20896)
@@ -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: trunk/Jmol/src/org/jmol/script/SV.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/SV.java 2015-12-20 22:01:37 UTC (rev
20895)
+++ trunk/Jmol/src/org/jmol/script/SV.java 2015-12-20 22:03:44 UTC (rev
20896)
@@ -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;
}
}
@@ -1511,27 +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) };
@@ -1776,4 +1805,5 @@
+ (property instanceof SV ? PT.esc(key) + " : " + format(new SV[] {
null, (SV) property },
0) : PT.toJSON(key, property)) + "}";
}
+
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2015-12-20
22:01:37 UTC (rev 20895)
+++ trunk/Jmol/src/org/jmol/script/ScriptMathProcessor.java 2015-12-20
22:03:44 UTC (rev 20896)
@@ -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: trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-12-20 22:01:37 UTC
(rev 20895)
+++ trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-12-20 22:03:44 UTC
(rev 20896)
@@ -3545,7 +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: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-12-20 22:01:37 UTC
(rev 20895)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-12-20 22:03:44 UTC
(rev 20896)
@@ -460,8 +460,8 @@
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);
@@ -1945,14 +1945,14 @@
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) {
@@ -2792,8 +2792,7 @@
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;
Modified: trunk/Jmol/src/org/jmol/shape/AtomShape.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/AtomShape.java 2015-12-20 22:01:37 UTC
(rev 20895)
+++ trunk/Jmol/src/org/jmol/shape/AtomShape.java 2015-12-20 22:03:44 UTC
(rev 20896)
@@ -105,11 +105,11 @@
if (atoms == null) // vector values are ignored if there are none for a
model
return;
isActive = true;
- if (bsSizeSet == null)
- bsSizeSet = new BS();
boolean isVisible = (rd != null && rd.value != 0);
boolean isAll = (bsSelected == null);
int i0 = (isAll ? ac - 1 : bsSelected.nextSetBit(0));
+ if (bsSizeSet == null)
+ bsSizeSet = BS.newN(ac);
if (mads == null && i0 >= 0)
mads = new short[ac];
for (int i = i0; i >= 0; i = (isAll ? i - 1 : bsSelected.nextSetBit(i +
1)))
@@ -128,9 +128,8 @@
isActive = true;
short colix = C.getColixO(value);
byte pid = PAL.pidOf(value);
- if (bsColixSet == null)
- bsColixSet = new BS();
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ int n = checkColixLength(colix, bs.length());
+ for (int i = bs.nextSetBit(0); i >= 0 && i < n; i = bs.nextSetBit(i + 1))
setColixAndPalette(colix, pid, i);
return;
}
@@ -149,7 +148,8 @@
int i0 = bs.nextSetBit(0);
if (mads == null && i0 >= 0)
mads = new short[ac];
- for (int i = i0, pt = 0; i >= 0; i = bs.nextSetBit(i + 1), pt++) {
+ int n = checkColixLength(colixes == null ? 0 : C.BLACK, bs.length());
+ for (int i = i0, pt = 0; i >= 0 && i < n; i = bs.nextSetBit(i + 1),
pt++) {
short colix = (colixes == null ? 0 : colixes[pt]);
if (colix == 0)
colix = C.INHERIT_ALL;
@@ -200,15 +200,20 @@
setPropS(propertyName, value, bs);
}
- protected void setColixAndPalette(short colix, byte paletteID, int
atomIndex) {
- if (colixes == null || atomIndex >= colixes.length) {
- if (colix == C.INHERIT_ALL)
- return;
- colixes = AU.ensureLengthShort(colixes, atomIndex + 1);
- paletteIDs = AU.ensureLengthByte(paletteIDs, atomIndex + 1);
+ protected int checkColixLength(short colix, int n) {
+ n = Math.min(ac, n);
+ if (colix == C.INHERIT_ALL)
+ return (colixes == null ? 0 : colixes.length);
+ if (colixes == null || n > colixes.length) {
+ colixes = AU.ensureLengthShort(colixes, n);
+ paletteIDs = AU.ensureLengthByte(paletteIDs, n);
}
if (bsColixSet == null)
bsColixSet = BS.newN(ac);
+ return n;
+ }
+
+ protected void setColixAndPalette(short colix, byte paletteID, int
atomIndex) {
colixes[atomIndex] = colix = getColixI(colix, paletteID, atomIndex);
bsColixSet.setBitTo(atomIndex, colix != C.INHERIT_ALL);
paletteIDs[atomIndex] = paletteID;
Modified: trunk/Jmol/src/org/jmol/shape/Labels.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/Labels.java 2015-12-20 22:01:37 UTC (rev
20895)
+++ trunk/Jmol/src/org/jmol/shape/Labels.java 2015-12-20 22:03:44 UTC (rev
20896)
@@ -84,6 +84,8 @@
defaultColix = 0; //"none" -- inherit from atom
defaultBgcolix = 0; //"none" -- off
defaultOffset = JC.LABEL_DEFAULT_OFFSET;
+ defaultAlignment = JC.TEXT_ALIGN_LEFT;
+ defaultPointer = JC.LABEL_POINTER_NONE;
defaultZPos = 0;
translucentAllowed = false;
}
@@ -101,10 +103,12 @@
if ("color" == propertyName) {
byte pid = PAL.pidOf(value);
short colix = C.getColixO(value);
- if (!setDefaults)
- for (int i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i = bsSelected
+ if (!setDefaults) {
+ int n = checkColixLength(colix, bsSelected.length());
+ for (int i = bsSelected.nextSetBit(0); i >= 0 && i < n; i = bsSelected
.nextSetBit(i + 1))
setLabelColix(i, colix, pid);
+ }
if (setDefaults || !defaultsOnlyForNone) {
defaultColix = colix;
defaultPaletteID = pid;
@@ -117,10 +121,9 @@
return;
float val = ((Float) value).floatValue();
float scalePixelsPerMicron = (val == 0 ? 0 : 10000f / val);
- for (int i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i = bsSelected
+ int n = Math.min(ac, strings.length);
+ for (int i = bsSelected.nextSetBit(0); i >= 0 && i < n; i = bsSelected
.nextSetBit(i + 1)) {
- if (strings.length <= i)
- continue;
Text text = getLabel(i);
if (text == null) {
text = Text.newLabel(vwr, null, strings[i], C.INHERIT_ALL, (short) 0,
@@ -136,15 +139,16 @@
if ("label" == propertyName) {
setScaling();
LabelToken[][] tokens = null;
+ int nbs = checkStringLength(bsSelected.length());
if (value instanceof Lst) {
Lst<SV> list = (Lst<SV>) value;
int n = list.size();
tokens = new LabelToken[][] { null };
- for (int pt = 0, i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i =
bsSelected
+ for (int pt = 0, i = bsSelected.nextSetBit(0); i >= 0 && i < nbs; i =
bsSelected
.nextSetBit(i + 1)) {
if (pt >= n) {
setLabel(nullToken, "", i, true);
- return;
+ continue;
}
tokens[0] = null;
setLabel(tokens, SV.sValue(list.get(pt++)), i, true);
@@ -160,19 +164,16 @@
return;
}
-// see label:
-// if ("labels" == propertyName) {
-// setScaling();
-// Lst<String> labels = (Lst<String>) value;
-// for (int i = bsSelected.nextSetBit(0), pt = 0; i >= 0 && i < ac; i =
bsSelected
-// .nextSetBit(i + 1)) {
-// String strLabel = labels.get(pt++);
-// LabelToken[][] tokens = (strLabel == null || strLabel.length() == 0
? nullToken
-// : new LabelToken[][] { null });
-// setLabel(tokens, strLabel, i, true);
-// }
-// return;
-// }
+ if (propertyName.startsWith("label:")) {
+ // from @1.label = "xxx"
+ setScaling();
+ // in principle, we could make this more efficient,
+ // it would be at the cost of general atom property setting
+ checkStringLength(ac);
+ setLabel(new LabelToken[][] { null }, propertyName.substring(6),
+ ((Integer) value).intValue(), false);
+ return;
+ }
if ("clearBoxes" == propertyName) {
labelBoxes = null;
@@ -187,12 +188,14 @@
if ("bgcolor" == propertyName) {
isActive = true;
if (bsBgColixSet == null)
- bsBgColixSet = new BS();
+ bsBgColixSet = BS.newN(ac);
short bgcolix = C.getColixO(value);
- if (!setDefaults)
- for (int i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i = bsSelected
+ if (!setDefaults) {
+ int n = checkBgColixLength(bgcolix, bsSelected.length());
+ for (int i = bsSelected.nextSetBit(0); i >= 0 && i < n; i = bsSelected
.nextSetBit(i + 1))
setBgcolix(i, bgcolix);
+ }
if (setDefaults || !defaultsOnlyForNone)
defaultBgcolix = bgcolix;
return;
@@ -201,7 +204,7 @@
// the rest require bsFontSet setting
if (bsFontSet == null)
- bsFontSet = new BS();
+ bsFontSet = BS.newN(ac);
if ("fontsize" == propertyName) {
int fontsize = ((Integer) value).intValue();
@@ -232,10 +235,11 @@
if ("offset" == propertyName) {
if (!(value instanceof Integer)) {
- if (!setDefaults)
+ if (!setDefaults) {
for (int i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i =
bsSelected
.nextSetBit(i + 1))
setPymolOffset(i, (float[]) value);
+ }
return;
}
@@ -250,12 +254,11 @@
}
if ("align" == propertyName) {
+ // note that if the label is not offset, this centers the label with
offset 0 0
String type = (String) value;
- int hAlignment = JC.TEXT_ALIGN_LEFT;
- if (type.equalsIgnoreCase("right"))
- hAlignment = JC.TEXT_ALIGN_RIGHT;
- else if (type.equalsIgnoreCase("center"))
- hAlignment = JC.TEXT_ALIGN_CENTER;
+ int hAlignment = (type.equalsIgnoreCase("right") ? JC.TEXT_ALIGN_RIGHT
+ : type.equalsIgnoreCase("center") ? JC.TEXT_ALIGN_CENTER
+ : JC.TEXT_ALIGN_LEFT);
for (int i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i = bsSelected
.nextSetBit(i + 1))
setHorizAlignment(i, hAlignment);
@@ -309,17 +312,19 @@
LabelToken[] tokensUNK = null;
String strLabel;
LabelToken[] tokens;
+ int nstr = checkStringLength(bsSelected.length());
+ short bgcolix = defaultBgcolix;
+ int nbg = checkBgColixLength(bgcolix, bsSelected.length());
+ short thisMad = (short) (mode >= 0 ? 1 : -1);
for (int i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i = bsSelected
.nextSetBit(i + 1)) {
Atom atom = atoms[i];
- if (formats == null || i >= formats.length)
- formats = AU.ensureLengthS(formats, i + 1);
- if (strings != null && strings.length > i && strings[i] != null) {
- mads[i] = (short) (mode == 0 && mads[i] < 0 || mode == 1 ? 1 : -1);
+ if (i < nstr && strings[i] != null) {
+ // an old string -- toggle
+ mads[i] = (short) (mode == 1 || mode == 0 && mads[i] < 0 ? 1 : -1);
} else {
- if (bsSizeSet == null)
- bsSizeSet = new BS();
- strings = AU.ensureLengthS(strings, i + 1);
+ // a new string -- turn on
+ mads[i] = thisMad;
if (atom.getGroup3(false).equals("UNK")) {
if (strLabelUNK == null) {
strLabelUNK = vwr.getStandardLabelFormat(1);
@@ -339,37 +344,20 @@
null, ptTemp);
formats[i] = strLabel;
bsSizeSet.set(i);
- if ((bsBgColixSet == null || !bsBgColixSet.get(i))
- && defaultBgcolix != 0)
+ if (i < nbg && !bsBgColixSet.get(i))
setBgcolix(i, defaultBgcolix);
- mads[i] = (short) (mode >= 0 ? 1 : -1);
}
setShapeVisibility(atom, strings != null && i < strings.length
&& strings[i] != null && mads[i] >= 0);
- // } else if (strings != null && atomIndex < strings.length) {
- // strings[atomIndex] = null;
}
return;
}
- if (propertyName.startsWith("label:")) {
- // from @1.label = "xxx"
- setScaling();
- setLabel(new LabelToken[1][], propertyName.substring(6),
- ((Integer) value).intValue(), false);
+ if ("pymolLabels" == propertyName) {
+ setPymolLabels((Map<Integer, Text>) value, bsSelected);
return;
}
- if ("textLabels" == propertyName) {
- // from PyMOL reader
- setScaling();
- Map<Integer, Text> labels = (Map<Integer, Text>) value;
- for (int i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i = bsSelected
- .nextSetBit(i + 1))
- setTextLabel(i, labels.get(Integer.valueOf(i)), null);
- return;
- }
-
if (propertyName == "deleteModelAtoms") {
labelBoxes = null;
int firstAtomDeleted = ((int[]) ((Object[]) value)[2])[1];
@@ -392,10 +380,47 @@
}
+ private int checkStringLength(int n) {
+ n = Math.min(ac, n);
+ if (strings == null || n > strings.length) {
+ formats = AU.ensureLengthS(formats, n);
+ strings = AU.ensureLengthS(strings, n);
+ if (bsSizeSet == null)
+ bsSizeSet = BS.newN(n);
+ }
+ return n;
+ }
+
+ private int checkBgColixLength(short colix, int n) {
+ n = Math.min(ac, n);
+ if (colix == C.INHERIT_ALL)
+ return (bgcolixes == null ? 0 : bgcolixes.length);
+ if (bgcolixes == null || n > bgcolixes.length)
+ bgcolixes = AU.ensureLengthShort(bgcolixes, n);
+ return n;
+ }
+
+ private void setPymolLabels(Map<Integer, Text> labels, BS bsSelected) {
+ // from PyMOL reader
+ setScaling();
+ int n = checkStringLength(ac);
+ for (int i = bsSelected.nextSetBit(0); i >= 0 && i < n; i = bsSelected
+ .nextSetBit(i + 1))
+ setPymolLabel(i, labels.get(Integer.valueOf(i)), null);
+ }
+
+ /**
+ * Sets offset using PyMOL standard array;
+ * only operates in cases where label is already defined
+ *
+ * @param i
+ * @param value
+ */
private void setPymolOffset(int i, float[] value) {
+ // from PyMOL reader or from set labeloffset [...]
Text text = getLabel(i);
if (text == null) {
- if (strings == null || strings.length <= i || strings[i] == null)
+ if (strings == null || i >= strings.length || strings[i] == null)
return;
byte fid = (bsFontSet != null && bsFontSet.get(i) ? fids[i] : -1);
if (fid < 0)
@@ -403,9 +428,7 @@
text = Text.newLabel(vwr, Font.getFont3D(fid), strings[i],
getColix2(i, atoms[i], false), getColix2(i, atoms[i], true), 0,
scalePixelsPerMicron);
- setTextLabel(i, text, formats[i]);
- if (text == null)
- return;
+ setPymolLabel(i, text, formats[i]);
}
text.pymolOffset = value;
}
@@ -418,13 +441,13 @@
private void setScaling() {
isActive = true;
if (bsSizeSet == null)
- bsSizeSet = new BS();
+ bsSizeSet = BS.newN(ac);
isScaled = vwr.getBoolean(T.fontscaling);
scalePixelsPerMicron = (isScaled ? vwr
.getScalePixelsPerAngstrom(false) * 10000f : 0);
}
- private void setTextLabel(int i, Text t, String format) {
+ private void setPymolLabel(int i, Text t, String format) {
if (t == null)
return;
String label = t.getText();
@@ -438,6 +461,7 @@
}
private void setLabel(LabelToken[][] temp, String strLabel, int i, boolean
doAll) {
+ // checkStringLength must be first
Atom atom = atoms[i];
LabelToken[] tokens = temp[0];
if (tokens == null)
@@ -476,10 +500,6 @@
private boolean addString(Atom atom, int i, String label, String strLabel) {
setShapeVisibility(atom, label != null);
- if (strings == null || i >= strings.length)
- strings = AU.ensureLengthS(strings, i + 1);
- if (formats == null || i >= formats.length)
- formats = AU.ensureLengthS(formats, i + 1);
boolean notNull = (strLabel != null);
boolean isNew = (strings[i] == null);
strings[i] = label;
@@ -533,11 +553,6 @@
}
private void setBgcolix(int i, short bgcolix) {
- if (bgcolixes == null || i >= bgcolixes.length) {
- if (bgcolix == 0)
- return;
- bgcolixes = AU.ensureLengthShort(bgcolixes, i + 1);
- }
bgcolixes[i] = bgcolix;
bsBgColixSet.setBitTo(i, bgcolix != 0);
Text text = getLabel(i);
@@ -548,12 +563,10 @@
private void setOffsets(int i, int offset) {
if (offsets == null || i >= offsets.length) {
- if (offset == 0)
+ if (offset == JC.LABEL_DEFAULT_OFFSET)
return;
- offsets = AU.ensureLengthI(offsets, i + 1);
+ offsets = AU.ensureLengthI(offsets, ac);
}
- if (offset == 0)
- offset = JC.LABEL_DEFAULT_OFFSET;
offsets[i] = (offsets[i] & JC.LABEL_FLAGS) | offset;
Text text = getLabel(i);
@@ -563,10 +576,15 @@
private void setHorizAlignment(int i, int hAlign) {
if (offsets == null || i >= offsets.length) {
- if (hAlign == JC.TEXT_ALIGN_LEFT)
+ switch (hAlign) {
+ case JC.TEXT_ALIGN_NONE:
+ case JC.TEXT_ALIGN_LEFT:
return;
- offsets = AU.ensureLengthI(offsets, i + 1);
+ }
+ offsets = AU.ensureLengthI(offsets, ac);
}
+ if (hAlign == JC.TEXT_ALIGN_NONE)
+ hAlign = JC.TEXT_ALIGN_LEFT;
offsets[i] = JC.setHorizAlignment(offsets[i], hAlign);
Text text = getLabel(i);
if (text != null)
@@ -577,7 +595,7 @@
if (offsets == null || i >= offsets.length) {
if (pointer == JC.LABEL_POINTER_NONE)
return;
- offsets = AU.ensureLengthI(offsets, i + 1);
+ offsets = AU.ensureLengthI(offsets, ac);
}
offsets[i] = JC.setPointer(offsets[i], pointer);
Text text = getLabel(i);
@@ -589,7 +607,7 @@
if (offsets == null || i >= offsets.length) {
if (!TF)
return;
- offsets = AU.ensureLengthI(offsets, i + 1);
+ offsets = AU.ensureLengthI(offsets, ac);
}
offsets[i] = JC.setZPosition(offsets[i], TF ? flag : 0);
}
@@ -598,7 +616,7 @@
if (fids == null || i >= fids.length) {
if (fid == zeroFontId)
return;
- fids = AU.ensureLengthByte(fids, i + 1);
+ fids = AU.ensureLengthByte(fids, ac);
}
fids[i] = fid;
bsFontSet.set(i);
Modified: trunk/Jmol/src/org/jmol/util/GenericApplet.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/GenericApplet.java 2015-12-20 22:01:37 UTC
(rev 20895)
+++ trunk/Jmol/src/org/jmol/util/GenericApplet.java 2015-12-20 22:03:44 UTC
(rev 20896)
@@ -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: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-20 22:01:37 UTC
(rev 20895)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-20 22:03:44 UTC
(rev 20896)
@@ -62,8 +62,16 @@
TODO: consider if models with no atoms will cause issues in relation to
model.firstAtomIndex
-Jmol.___JmolVersion="14.5.1_2015.12.14"
+Jmol.___JmolVersion="14.5.1_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="14.5.1_2015.12.14"
+
bug fix: JSmol (JSmolCore.js) check for MS Edge browser, which does not
support dataURI
JmolVersion="14.5.0_2015.12.13"
Modified: trunk/Jmol/src/org/jmol/viewer/StatusManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2015-12-20 22:01:37 UTC
(rev 20895)
+++ trunk/Jmol/src/org/jmol/viewer/StatusManager.java 2015-12-20 22:03:44 UTC
(rev 20896)
@@ -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: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-12-20 22:01:37 UTC (rev
20895)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-12-20 22:03:44 UTC (rev
20896)
@@ -4641,9 +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.
*
@@ -5746,7 +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;
}
}
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