Revision: 20687
http://sourceforge.net/p/jmol/code/20687
Author: hansonr
Date: 2015-08-10 00:15:14 +0000 (Mon, 10 Aug 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.3.15_2015.08.09"
bug fix: CML reader can fail (e.g. nsc244a.cml)
code: refactoring of JmolDataManager
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java
trunk/Jmol/src/org/jmol/api/JmolDataManager.java
trunk/Jmol/src/org/jmol/modelset/LabelToken.java
trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
trunk/Jmol/src/org/jmol/script/ScriptExpr.java
trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
trunk/Jmol/src/org/jmol/scriptext/MathExt.java
trunk/Jmol/src/org/jmol/util/Escape.java
trunk/Jmol/src/org/jmol/viewer/DataManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
trunk/Jmol/src/org/jmol/viewer/StateCreator.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
2015-08-08 21:47:59 UTC (rev 20686)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlCmlReader.java
2015-08-10 00:15:14 UTC (rev 20687)
@@ -292,12 +292,12 @@
if (atts.containsKey("atomRef1")) {
breakOutBondTokens(atts.get("atomRef1"));
for (int i = tokenCount; --i >= 0;)
- bondArray[i].atomIndex1 = asc.getAtomIndex(tokens[i]);
+ bondArray[i].atomIndex1 = getAtomIndex(tokens[i]);
}
if (atts.containsKey("atomRef2")) {
breakOutBondTokens(atts.get("atomRef2"));
for (int i = tokenCount; --i >= 0;)
- bondArray[i].atomIndex2 = asc.getAtomIndex(tokens[i]);
+ bondArray[i].atomIndex2 = getAtomIndex(tokens[i]);
}
} else if (name.equals("atomarray")) {
state = MOLECULE_ATOM_ARRAY;
@@ -442,6 +442,10 @@
}
}
+ private int getAtomIndex(String label) {
+ return asc.getAtomIndex(isSerial ? label.substring(1) : label);
+ }
+
final private static String[] unitCellParamTags = { "a", "b", "c", "alpha",
"beta", "gamma" };
Modified: trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java 2015-08-08
21:47:59 UTC (rev 20686)
+++ trunk/Jmol/src/org/jmol/adapter/readers/xml/XmlReader.java 2015-08-10
00:15:14 UTC (rev 20687)
@@ -153,7 +153,7 @@
try {
thisReader.processXml(this, saxReader);
} catch (Exception e) {
- return "Error reading XML: " + (parent.vwr.isJS ? e : e.getMessage());
+ return "Error reading XML: " + ((parent == null ? vwr : parent.vwr).isJS
? e : e.getMessage());
}
return null;
}
Modified: trunk/Jmol/src/org/jmol/api/JmolDataManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolDataManager.java 2015-08-08 21:47:59 UTC
(rev 20686)
+++ trunk/Jmol/src/org/jmol/api/JmolDataManager.java 2015-08-10 00:15:14 UTC
(rev 20687)
@@ -9,11 +9,18 @@
public interface JmolDataManager {
+ public static final int DATA_TYPE_LAST = -2;
public final static int DATA_TYPE_UNKNOWN = -1;
public final static int DATA_TYPE_STRING = 0;
public final static int DATA_TYPE_AF = 1;
public final static int DATA_TYPE_AFF = 2;
public final static int DATA_TYPE_AFFF = 3;
+ // indexes into Object[] data
+ public final static int DATA_LABEL = 0;
+ public final static int DATA_VALUE = 1;
+ public final static int DATA_SELECTION = 2;
+ public final static int DATA_TYPE = 3;
+ public final static int DATA_SAVE_IN_STATE = 4; // optional; defaults to TRUE
JmolDataManager set(Viewer vwr);
@@ -21,22 +28,16 @@
void clear();
- Object[] getData(String type);
+ void deleteModelAtoms(int firstAtomIndex, int nAtoms, BS bsDeleted);
- float[][] getDataFloat2D(String label);
+ Object getData(String label, BS bsSelected, int dataType);
- float[][][] getDataFloat3D(String label);
+ float getDataFloatAt(String label, int atomIndex);
- float getDataFloat(String label, int atomIndex);
-
- float[] getDataFloatA(String label, BS bsSelected);
-
String getDefaultVdwNameOrData(VDW type, BS bs);
- void deleteModelAtoms(int firstAtomIndex, int nAtoms, BS bsDeleted);
+ void setData(String type, Object[] data, int dataType, int ac,
+ int matchField, int matchFieldColumnCount, int dataField,
+ int dataFieldColumnCount);
- void setData(String type, Object[] data, int arrayCount, int ac,
- int matchField, int matchFieldColumnCount, int field,
- int fieldColumnCount);
-
}
Modified: trunk/Jmol/src/org/jmol/modelset/LabelToken.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/LabelToken.java 2015-08-08 21:47:59 UTC
(rev 20686)
+++ trunk/Jmol/src/org/jmol/modelset/LabelToken.java 2015-08-10 00:15:14 UTC
(rev 20687)
@@ -37,6 +37,7 @@
import javajs.util.SB;
import javajs.util.T3;
+import org.jmol.api.JmolDataManager;
import org.jmol.script.SV;
import org.jmol.script.T;
import org.jmol.util.Edge;
@@ -405,10 +406,10 @@
String propertyName = strFormat.substring(ich, ichClose).toLowerCase();
if (propertyName.startsWith("property_")) {
lt.tok = T.data;
- lt.data = vwr.getDataFloat(propertyName, null);
+ lt.data = vwr.getDataObj(propertyName, null,
JmolDataManager.DATA_TYPE_AF);
} else if (propertyName.startsWith("validation.")) {
lt.tok = T.validation;
- lt.data = vwr.getDataFloat("property_" + propertyName.substring(11),
null);
+ lt.data = vwr.getDataObj("property_" + propertyName.substring(11),
null, JmolDataManager.DATA_TYPE_AF);
} else {
T token = T.getTokenFromName(propertyName);
if (token != null && isLabelPropertyTok(token.tok))
@@ -427,11 +428,11 @@
break;
}
String s = strFormat.substring(ich, ichCloseBracket);
- lt.data = vwr.getDataFloat(s, null);
+ lt.data = vwr.getDataObj(s, null, JmolDataManager.DATA_TYPE_AF);
// TODO untested j2s issue fix
if (lt.data == null) {
- lt.data = vwr.getData(s);
- if (lt.data instanceof Object[]) {// either that or it is null
+ lt.data = vwr.getDataObj(s, null, JmolDataManager.DATA_TYPE_UNKNOWN);
+ if (lt.data != null) {
lt.data = ((Object[]) lt.data)[1];
if (lt.data instanceof String)
lt.data = PT.split((String) lt.data, "\n");
Modified: trunk/Jmol/src/org/jmol/modelset/ModelLoader.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-08-08 21:47:59 UTC
(rev 20686)
+++ trunk/Jmol/src/org/jmol/modelset/ModelLoader.java 2015-08-10 00:15:14 UTC
(rev 20687)
@@ -458,8 +458,8 @@
}
key = "property_" + key.toLowerCase();
Logger.info("creating " + key + " for model " + ms.getModelName(i));
- vwr.setData(key, new Object[] { key, value, bs,
Integer.valueOf(JmolDataManager.DATA_TYPE_UNKNOWN), Boolean.FALSE }, ms.ac, 0,
- 0, Integer.MAX_VALUE, 0);
+ vwr.setData(key, new Object[] { key, value, bs,
Integer.valueOf(JmolDataManager.DATA_TYPE_UNKNOWN), Boolean.FALSE },
+ ms.ac, 0, 0, Integer.MAX_VALUE, 0);
}
}
}
@@ -839,7 +839,8 @@
Logger.info(nRead + " atoms created");
}
- private void addJmolDataProperties(Model m, Map<String, float[]>
jmolDataProperties) {
+ private void addJmolDataProperties(Model m,
+ Map<String, float[]> jmolDataProperties) {
if (jmolDataProperties == null)
return;
BS bs = m.bsAtoms;
@@ -849,17 +850,28 @@
float[] data = e.getValue();
if (data.length != nAtoms)
return;
- if (PT.isOneOf(key, ";x;y;z;"))
+ int tok = (key.startsWith("property_") ? T.property : T
+ .getTokFromName(key));
+ switch (tok) {
+ default:
+ if (T.tokAttr(tok, T.settable)) {
+ vwr.setAtomProperty(bs, tok, 0, 0, null, data, null);
+ break;
+ }
+ // not settable -- must encode as property_
+ //$FALL-THROUGH$
+ case T.x:
+ case T.y:
+ case T.z:
key = "property_" + key;
- if (key.startsWith("property_")) {
+ tok = T.property;
+ //$FALL-THROUGH$
+ case T.property:
+ // must create data set
vwr.setData(
key,
new Object[] { key, data, bs,
Integer.valueOf(JmolDataManager.DATA_TYPE_AF) }, 0, 0, 0, 0,
0);
- } else {
- int tok = T.getTokFromName(key);
- if (T.tokAttr(tok, T.settable))
- vwr.setAtomProperty(bs, tok, 0, 0, null, data, null);
}
}
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptExpr.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-08-08 21:47:59 UTC
(rev 20686)
+++ trunk/Jmol/src/org/jmol/script/ScriptExpr.java 2015-08-10 00:15:14 UTC
(rev 20687)
@@ -966,7 +966,7 @@
if (pc + 2 == code.length)
invArg();
if (!chk)
- data = vwr.getDataFloat((String) code[++pc].value, null);
+ data = (float[]) vwr.getDataObj((String) code[++pc].value, null,
JmolDataManager.DATA_TYPE_AF);
}
if (++pc == code.length)
invArg(); // compiler would not let this happen, actually
@@ -1647,7 +1647,7 @@
ptT = new P3();
break;
case T.property:
- data = vwr.getDataFloat((String) opValue, null);
+ data = (float[]) vwr.getDataObj((String) opValue, null,
JmolDataManager.DATA_TYPE_AF);
break;
}
Modified: trunk/Jmol/src/org/jmol/scriptext/CmdExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-08-08 21:47:59 UTC
(rev 20686)
+++ trunk/Jmol/src/org/jmol/scriptext/CmdExt.java 2015-08-10 00:15:14 UTC
(rev 20687)
@@ -1923,8 +1923,7 @@
default:
eval.bad();
}
- String dataType = dataLabel + " ";
- dataType = dataType.substring(0, dataType.indexOf(" ")).toLowerCase();
+ String dataType = dataLabel.substring(0, (dataLabel + " ").indexOf("
")).toLowerCase();
if (dataType.equals("model") || dataType.equals("append")) {
eval.cmdLoad();
return;
@@ -1952,30 +1951,30 @@
// not saving this data in the state?
if (dataType.equals("element_vdw")) {
// vdw for now
- d[0] = dataType;
- d[1] = dataString.replace(';', '\n');
+ d[JmolDataManager.DATA_LABEL] = dataType;
+ d[JmolDataManager.DATA_VALUE] = dataString.replace(';', '\n');
int n = Elements.elementNumberMax;
int[] eArray = new int[n + 1];
for (int ie = 1; ie <= n; ie++)
eArray[ie] = ie;
- d[2] = eArray;
- d[3] = Integer.valueOf(JmolDataManager.DATA_TYPE_STRING);
+ d[JmolDataManager.DATA_SELECTION] = eArray;
+ d[JmolDataManager.DATA_TYPE] =
Integer.valueOf(JmolDataManager.DATA_TYPE_STRING);
vwr.setData("element_vdw", d, n, 0, 0, 0, 0);
return;
}
if (dataType.indexOf("data2d_") == 0) {
// data2d_someName
- d[0] = dataLabel;
- d[1] = parseDataArray(dataString, false);
- d[3] = Integer.valueOf(JmolDataManager.DATA_TYPE_AFF);
+ d[JmolDataManager.DATA_LABEL] = dataLabel;
+ d[JmolDataManager.DATA_VALUE] = parseDataArray(dataString, false);
+ d[JmolDataManager.DATA_TYPE] =
Integer.valueOf(JmolDataManager.DATA_TYPE_AFF);
vwr.setData(dataLabel, d, 0, 0, 0, 0, 0);
return;
}
if (dataType.indexOf("data3d_") == 0) {
// data3d_someName
- d[0] = dataLabel;
- d[1] = parseDataArray(dataString, true);
- d[3] = Integer.valueOf(JmolDataManager.DATA_TYPE_AFFF);
+ d[JmolDataManager.DATA_LABEL] = dataLabel;
+ d[JmolDataManager.DATA_VALUE] = parseDataArray(dataString, true);
+ d[JmolDataManager.DATA_TYPE] =
Integer.valueOf(JmolDataManager.DATA_TYPE_AFFF);
vwr.setData(dataLabel, d, 0, 0, 0, 0, 0);
return;
}
@@ -1983,7 +1982,7 @@
if (dataType.indexOf("property_") == 0
&& !(tokens.length == 2 && tokens[1].equals("set"))) {
BS bs = vwr.bsA();
- d[0] = dataType;
+ d[JmolDataManager.DATA_LABEL] = dataType;
int atomNumberField = (isOneValue ? 0 : ((Integer) vwr
.getP("propertyAtomNumberField")).intValue());
int atomNumberFieldColumnCount = (isOneValue ? 0 : ((Integer) vwr
@@ -2027,12 +2026,12 @@
bsTemp.set(atomNo);
atomMap[atomNo] = j;
}
- d[2] = atomMap;
+ d[JmolDataManager.DATA_SELECTION] = atomMap;
} else {
- d[2] = BSUtil.copy(bs);
+ d[JmolDataManager.DATA_SELECTION] = BSUtil.copy(bs);
}
- d[1] = dataString;
- d[3] = Integer.valueOf(JmolDataManager.DATA_TYPE_STRING);
+ d[JmolDataManager.DATA_VALUE] = dataString;
+ d[JmolDataManager.DATA_TYPE] =
Integer.valueOf(JmolDataManager.DATA_TYPE_STRING);
vwr.setData(dataType, d, ac, atomNumberField,
atomNumberFieldColumnCount, propertyField, propertyFieldColumnCount);
return;
@@ -2040,15 +2039,15 @@
if ("occupany".equals(dataType))
dataType = "occupancy"; // legacy misspelling in states
int userType = AtomCollection.getUserSettableType(dataType);
- if (userType >= 0) {
+ if (userType > JmolDataManager.DATA_TYPE_UNKNOWN) {
// this is a known settable type or "property_xxxx"
vwr.setAtomData(userType, dataType, dataString, isDefault);
return;
}
// this is just information to be stored.
- d[0] = dataLabel;
- d[1] = dataString;
- d[3] = Integer.valueOf(JmolDataManager.DATA_TYPE_STRING);
+ d[JmolDataManager.DATA_LABEL] = dataLabel;
+ d[JmolDataManager.DATA_VALUE] = dataString;
+ d[JmolDataManager.DATA_TYPE] =
Integer.valueOf(JmolDataManager.DATA_TYPE_STRING);
vwr.setData(dataType, d, 0, 0, 0, 0, 0);
}
@@ -4310,9 +4309,9 @@
case T.data:
String dtype = ((len = slen) == 3 ? paramAsStr(2) : null);
if (!chk) {
- Object[] data = vwr.getData(dtype);
+ Object[] data = (Object[]) vwr.getDataObj(dtype, null,
JmolDataManager.DATA_TYPE_LAST);
msg = (data == null ? "no data" : Escape.encapsulateData(
- (String) data[0], data[1], ((Integer) data[3]).intValue()));
+ (String) data[JmolDataManager.DATA_LABEL],
data[JmolDataManager.DATA_VALUE], ((Integer)
data[JmolDataManager.DATA_TYPE]).intValue()));
}
break;
case T.spacegroup:
@@ -4993,10 +4992,10 @@
float min, float max)
throws ScriptException {
- float[] data = (property == null ?
- (float[]) e.getBitsetProperty(bs, tok, null, null, null, null,
+ float[] data = (float[]) (property == null ?
+ e.getBitsetProperty(bs, tok, null, null, null, null,
false, Integer.MAX_VALUE, false)
- : vwr.getDataFloat(property, bs));
+ : vwr.getDataObj(property, bs, JmolDataManager.DATA_TYPE_AF));
if (!Float.isNaN(min))
for (int i = 0; i < data.length; i++)
if (data[i] < min)
Modified: trunk/Jmol/src/org/jmol/scriptext/IsoExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-08-08 21:47:59 UTC
(rev 20686)
+++ trunk/Jmol/src/org/jmol/scriptext/IsoExt.java 2015-08-10 00:15:14 UTC
(rev 20687)
@@ -28,6 +28,7 @@
import java.util.Map;
import org.jmol.api.Interface;
+import org.jmol.api.JmolDataManager;
import org.jmol.api.MepCalculationInterface;
import org.jmol.api.SymmetryInterface;
import org.jmol.atomdata.RadiusData;
@@ -1440,7 +1441,7 @@
data = new float[vwr.ms.ac];
if (chk)
continue;
- data = vwr.getDataFloat(str, null);
+ data = (float[]) vwr.getDataObj(str, null,
JmolDataManager.DATA_TYPE_AF);
if (data == null)
invArg();
addShapeProperty(propertyList, propertyName, data);
@@ -2136,7 +2137,7 @@
nZ = Math.abs(nZ);
xyzdata = floatArraySetXYZ(++eval.iToken, nX, nY, nZ);
} else if (isXYZV) {
- xyzdata = vwr.getDataFloat3D(name);
+ xyzdata = (float[][][]) vwr.getDataObj(name, null,
JmolDataManager.DATA_TYPE_AFFF);
} else {
xyzdata = vwr.functionXYZ(name, nX, nY, nZ);
}
@@ -2163,7 +2164,7 @@
nY = Math.abs(nY);
fdata = floatArraySet(++eval.iToken, nX, nY);
} else if (isXYZ) {
- fdata = vwr.getDataFloat2D(name);
+ fdata = (float[][]) vwr.getDataObj(name, null,
JmolDataManager.DATA_TYPE_AFF);
nX = (fdata == null ? 0 : fdata.length);
nY = 3;
} else {
Modified: trunk/Jmol/src/org/jmol/scriptext/MathExt.java
===================================================================
--- trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-08-08 21:47:59 UTC
(rev 20686)
+++ trunk/Jmol/src/org/jmol/scriptext/MathExt.java 2015-08-10 00:15:14 UTC
(rev 20687)
@@ -32,6 +32,7 @@
import java.util.regex.Pattern;
import org.jmol.api.Interface;
+import org.jmol.api.JmolDataManager;
import org.jmol.api.JmolNMRInterface;
import org.jmol.api.JmolPatternMatcher;
import org.jmol.atomdata.RadiusData;
@@ -773,7 +774,7 @@
}
if (selected.indexOf("data2d_") == 0) {
// tab, newline separated data
- float[][] f1 = vwr.getDataFloat2D(selected);
+ float[][] f1 = (float[][]) vwr.getDataObj(selected, null,
JmolDataManager.DATA_TYPE_AFF);
if (f1 == null)
return mp.addXStr("");
if (args.length == 2 && args[1].tok == T.integer) {
@@ -790,10 +791,10 @@
// parallel mp.addition of float property data sets
if (selected.indexOf("property_") == 0) {
- float[] f1 = vwr.getDataFloat(selected, null);
+ float[] f1 = (float[]) vwr.getDataObj(selected, null,
JmolDataManager.DATA_TYPE_AF);
if (f1 == null)
return mp.addXStr("");
- float[] f2 = (type.indexOf("property_") == 0 ? vwr.getDataFloat(type,
null)
+ float[] f2 = (type.indexOf("property_") == 0 ? (float[])
vwr.getDataObj(selected, null, JmolDataManager.DATA_TYPE_AF)
: null);
if (f2 != null) {
f1 = AU.arrayCopyF(f1, -1);
@@ -806,7 +807,7 @@
// some other data type -- just return it
//if (args.length == 1) {
- Object[] data = vwr.getData(selected);
+ Object[] data = (Object[]) vwr.getDataObj(selected, null,
JmolDataManager.DATA_TYPE_UNKNOWN);
return mp.addXStr(data == null ? "" : "" + data[1]);
// }
}
Modified: trunk/Jmol/src/org/jmol/util/Escape.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Escape.java 2015-08-08 21:47:59 UTC (rev
20686)
+++ trunk/Jmol/src/org/jmol/util/Escape.java 2015-08-10 00:15:14 UTC (rev
20687)
@@ -42,6 +42,7 @@
import javajs.util.T3;
import javajs.util.V3;
+import org.jmol.api.JmolDataManager;
import org.jmol.java.BS;
import org.jmol.script.SV;
import org.jmol.script.T;
@@ -535,12 +536,23 @@
}
public static String encapsulateData(String name, Object data, int depth) {
- return " DATA \"" + name + "\"\n" +
- (depth == 2 ?
- escapeFloatAA((float[][]) data, true) + ";\n"
- : depth == 3 ?
- escapeFloatAAA((float[][][]) data, true) + ";\n"
- : data) + " END \"" + name + "\";\n";
+ String s;
+ switch (depth) {
+ case JmolDataManager.DATA_TYPE_AF:
+ s = escapeFloatA((float[]) data, false) + ";\n";
+ break;
+ case JmolDataManager.DATA_TYPE_AFF:
+ s = escapeFloatAA((float[][]) data, true) + ";\n";
+ break;
+ case JmolDataManager.DATA_TYPE_AFFF:
+ s = escapeFloatAAA((float[][][]) data, true) + ";\n";
+ break;
+ default:
+ s = data.toString();
+ break;
+ }
+ return " DATA \"" + name + "\"\n" + s + " END \"" + name + "\";\n";
+
}
// public static String escapeXml(Object value) {
Modified: trunk/Jmol/src/org/jmol/viewer/DataManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/DataManager.java 2015-08-08 21:47:59 UTC
(rev 20686)
+++ trunk/Jmol/src/org/jmol/viewer/DataManager.java 2015-08-10 00:15:14 UTC
(rev 20687)
@@ -41,7 +41,6 @@
import javajs.util.PT;
import javajs.util.SB;
-
/*
* a class for storing and retrieving user data,
* including atom-related and color-related data
@@ -51,13 +50,13 @@
public class DataManager implements JmolDataManager {
private Map<String, Object[]> dataValues = new Hashtable<String, Object[]>();
-
+
private Viewer vwr;
-
+
public DataManager() {
// for reflection
}
-
+
@Override
public JmolDataManager set(Viewer vwr) {
this.vwr = vwr;
@@ -68,13 +67,7 @@
public void clear() {
dataValues.clear();
}
-
- //private final static int DATA_LABEL = 0;
- private final static int DATA_VALUE = 1;
- private final static int DATA_SELECTION_MAP = 2;
- private final static int DATA_TYPE = 3;
- private final static int DATA_SAVE_IN_STATE = 4;
-
+
/**
* This method needs to be redone using a class instead of Object[]
*/
@@ -102,7 +95,7 @@
}
type = type.toLowerCase();
if (type.equals("element_vdw")) {
- String stringData = ((String) data[DATA_VALUE]).trim();
+ String stringData = ((String) data[JmolDataManager.DATA_VALUE]).trim();
if (stringData.length() == 0) {
vwr.userVdwMars = null;
vwr.userVdws = null;
@@ -112,27 +105,27 @@
if (vwr.bsUserVdws == null)
vwr.setUserVdw(vwr.defaultVdw);
Parser.parseFloatArrayFromMatchAndField(stringData, vwr.bsUserVdws, 1, 0,
- (int[]) data[DATA_SELECTION_MAP], 2, 0, vwr.userVdws, 1);
+ (int[]) data[JmolDataManager.DATA_SELECTION], 2, 0, vwr.userVdws, 1);
for (int i = vwr.userVdws.length; --i >= 0;)
vwr.userVdwMars[i] = (int) Math.floor(vwr.userVdws[i] * 1000);
return;
}
- int depth = ((Integer) data[DATA_TYPE]).intValue();
- Object val = data[DATA_VALUE];
+ int depth = getType(data);
+ Object val = data[JmolDataManager.DATA_VALUE];
if (depth == JmolDataManager.DATA_TYPE_UNKNOWN)
- data[DATA_TYPE] = Integer
+ data[JmolDataManager.DATA_TYPE] = Integer
.valueOf(depth = (val instanceof String ?
JmolDataManager.DATA_TYPE_STRING
: AU.isAF(val) ? JmolDataManager.DATA_TYPE_AF
: AU.isAFF(val) ? JmolDataManager.DATA_TYPE_AFF : AU
.isAFFF(val) ? JmolDataManager.DATA_TYPE_AFFF
: JmolDataManager.DATA_TYPE_UNKNOWN));
- if (data[DATA_SELECTION_MAP] != null && arrayCount > 0) {
+ if (data[JmolDataManager.DATA_SELECTION] != null && arrayCount > 0) {
boolean createNew = (matchField != 0 || field != Integer.MIN_VALUE
&& field != Integer.MAX_VALUE);
Object[] oldData = dataValues.get(type);
BS bs;
float[] f = (oldData == null || createNew ? new float[actualAtomCount]
- : AU.ensureLengthA(((float[]) oldData[1]), actualAtomCount));
+ : AU.ensureLengthA(((float[]) oldData[JmolDataManager.DATA_VALUE]),
actualAtomCount));
// check to see if the data COULD be interpreted as a string of float
values
// and if so, do that. This pre-fetches the tokens in that case.
@@ -149,14 +142,13 @@
if (field == Integer.MIN_VALUE
&& (strData = PT.getTokens(stringData)).length > 1)
field = 0;
-
if (field == Integer.MIN_VALUE) {
// set the selected data elements to a single value
- bs = (BS) data[DATA_SELECTION_MAP];
+ bs = (BS) data[JmolDataManager.DATA_SELECTION];
setSelectedFloats(PT.parseFloat(stringData), bs, f);
} else if (field == 0 || field == Integer.MAX_VALUE) {
// just get the selected token values
- bs = (BS) data[DATA_SELECTION_MAP];
+ bs = (BS) data[JmolDataManager.DATA_SELECTION];
if (floatData != null) {
int n = floatData.length;
if (n == bs.cardinality()) {
@@ -164,7 +156,8 @@
.nextSetBit(i + 1), pt++)
f[i] = floatData[pt];
} else {
- for (int i = bs.nextSetBit(0); i >= 0 && i < n; i =
bs.nextSetBit(i + 1))
+ for (int i = bs.nextSetBit(0); i >= 0 && i < n; i = bs
+ .nextSetBit(i + 1))
f[i] = floatData[i];
}
} else {
@@ -173,13 +166,13 @@
}
} else if (matchField <= 0) {
// get the specified field >= 1 for the selected atoms
- bs = (BS) data[DATA_SELECTION_MAP];
+ bs = (BS) data[JmolDataManager.DATA_SELECTION];
Parser.parseFloatArrayFromMatchAndField(stringData, bs, 0, 0, null,
field, fieldColumnCount, f, 1);
} else {
// get the selected field, with an integer match in a specified field
// in this case, bs is created and indicates which data points were set
- int[] iData = (int[]) data[DATA_SELECTION_MAP];
+ int[] iData = (int[]) data[JmolDataManager.DATA_SELECTION];
Parser.parseFloatArrayFromMatchAndField(stringData, null, matchField,
matchFieldColumnCount, iData, field, fieldColumnCount, f, 1);
bs = new BS();
@@ -187,12 +180,14 @@
if (iData[i] >= 0)
bs.set(iData[i]);
}
- if (oldData != null && oldData[DATA_SELECTION_MAP] instanceof BS
+ if (oldData != null
+ && oldData[JmolDataManager.DATA_SELECTION] instanceof BS
&& !createNew)
- bs.or((BS) (oldData[DATA_SELECTION_MAP]));
- data[DATA_TYPE] = Integer.valueOf(JmolDataManager.DATA_TYPE_AF);
- data[DATA_SELECTION_MAP] = bs;
- data[DATA_VALUE] = f;
+ bs.or((BS) (oldData[JmolDataManager.DATA_SELECTION]));
+ data[JmolDataManager.DATA_TYPE] = Integer
+ .valueOf(JmolDataManager.DATA_TYPE_AF);
+ data[JmolDataManager.DATA_SELECTION] = bs;
+ data[JmolDataManager.DATA_VALUE] = f;
if (type.indexOf("property_atom.") == 0) {
int tok = T.getSettableTokFromString(type = type.substring(14));
if (tok == T.nada) {
@@ -211,6 +206,10 @@
dataValues.put(type, data);
}
+ private int getType(Object[] data) {
+ return ((Integer) data[JmolDataManager.DATA_TYPE]).intValue();
+ }
+
/**
*
* @param f
@@ -220,52 +219,50 @@
private static void setSelectedFloats(float f, BS bs, float[] data) {
boolean isAll = (bs == null);
int i0 = (isAll ? 0 : bs.nextSetBit(0));
- for (int i = i0; i >= 0 && i < data.length; i = (isAll ? i + 1 :
bs.nextSetBit(i + 1)))
+ for (int i = i0; i >= 0 && i < data.length; i = (isAll ? i + 1 : bs
+ .nextSetBit(i + 1)))
data[i] = f;
}
@Override
- public Object[] getData(String type) {
- if (dataValues.size() == 0 || type == null)
+ public Object getData(String label, BS bsSelected, int dataType) {
+ if (dataValues.size() == 0 || label == null)
return null;
- if (!type.equalsIgnoreCase("types"))
- return dataValues.get(type);
- String[] info = new String[2];
- info[0] = "types";
- info[1] = "";
- int n = 0;
- for (String name : dataValues.keySet())
- info[1] += (n++ > 0 ? "\n" : "") + name;
- return info;
+ switch (dataType) {
+ case JmolDataManager.DATA_TYPE_UNKNOWN:
+ case JmolDataManager.DATA_TYPE_LAST:
+ if (!label.equalsIgnoreCase("types"))
+ return dataValues.get(label);
+ String[] info = new String[2];
+ info[JmolDataManager.DATA_LABEL] = "types";
+ info[JmolDataManager.DATA_VALUE] = "";
+ int nv = 0;
+ for (String name : dataValues.keySet())
+ info[JmolDataManager.DATA_VALUE] += (nv++ > 0 ? "\n" : "") + name;
+ return info;
+ default:
+ Object[] data = dataValues.get(label);
+ if (data == null || getType(data) != dataType)
+ return null;
+ if (bsSelected == null)
+ return data[JmolDataManager.DATA_VALUE];
+ // When bsSelected is not null, this returns a truncated array, which
must be of type float[]
+ float[] f = (float[]) data[JmolDataManager.DATA_VALUE];
+ float[] fnew = new float[bsSelected.cardinality()];
+ // load array
+ for (int i = 0, n = f.length, p = bsSelected.nextSetBit(0); p >= 0
+ && i < n; p = bsSelected.nextSetBit(p + 1))
+ fnew[i++] = f[p];
+ return fnew;
+ }
}
- /**
- * When bsSelected is not null, this returns a truncated array
- *
- */
@Override
- public float[] getDataFloatA(String label, BS bsSelected) {
- if (dataValues.size() == 0)
- return null;
- Object[] data = getData(label);
- if (data == null || ((Integer)data[DATA_TYPE]).intValue() !=
JmolDataManager.DATA_TYPE_AF)
- return null;
- float[] f = (float[]) data[DATA_VALUE];
- if (bsSelected == null)
- return f;
- float[] fnew = new float[bsSelected.cardinality()];
- // load array
- for (int i = 0, n = f.length, p = bsSelected.nextSetBit(0); p >= 0 && i <
n; p = bsSelected.nextSetBit(p + 1))
- fnew[i++] = f[p];
- return fnew;
- }
-
- @Override
- public float getDataFloat(String label, int atomIndex) {
+ public float getDataFloatAt(String label, int atomIndex) {
if (dataValues.size() > 0) {
- Object[] data = getData(label);
- if (data != null && ((Integer)data[DATA_TYPE]).intValue() ==
JmolDataManager.DATA_TYPE_AF) {
- float[] f = (float[]) data[DATA_VALUE];
+ Object[] data = (Object[]) getData(label, null, 0);
+ if (data != null && getType(data) == JmolDataManager.DATA_TYPE_AF) {
+ float[] f = (float[]) data[JmolDataManager.DATA_VALUE];
if (atomIndex < f.length)
return f[atomIndex];
}
@@ -274,46 +271,17 @@
}
@Override
- public float[][] getDataFloat2D(String label) {
- if (dataValues.size() == 0)
- return null;
- Object[] data = getData(label);
- if (data == null || ((Integer)data[DATA_TYPE]).intValue() !=
JmolDataManager.DATA_TYPE_AFF)
- return null;
- return (float[][]) data[DATA_VALUE];
- }
-
- @Override
- public float[][][] getDataFloat3D(String label) {
- if (dataValues.size() == 0)
- return null;
- Object[] data = getData(label);
- if (data == null || ((Integer)data[DATA_TYPE]).intValue() !=
JmolDataManager.DATA_TYPE_AFFF)
- return null;
- return (float[][][]) data[DATA_VALUE];
- }
-
- @Override
public void deleteModelAtoms(int firstAtomIndex, int nAtoms, BS bsDeleted) {
if (dataValues.size() == 0)
return;
- for (String name: dataValues.keySet()) {
+ for (String name : dataValues.keySet()) {
if (name.indexOf("property_") == 0) {
Object[] obj = dataValues.get(name);
- BSUtil.deleteBits((BS) obj[2], bsDeleted);
- switch (((Integer)obj[3]).intValue()) {
- case JmolDataManager.DATA_TYPE_AF:
- obj[1] = AU.deleteElements(obj[1], firstAtomIndex, nAtoms);
- break;
- case JmolDataManager.DATA_TYPE_AFF:
- obj[1] = AU.deleteElements(obj[1], firstAtomIndex, nAtoms);
- break;
- default:
- // is there anything else??
- break;
- }
+ BSUtil.deleteBits((BS) obj[DATA_SELECTION], bsDeleted);
+ obj[DATA_VALUE] = AU.deleteElements(obj[DATA_VALUE], firstAtomIndex,
+ nAtoms);
}
- }
+ }
}
@Override
@@ -325,10 +293,12 @@
int i1 = (isAll ? Elements.elementNumberMax : bs.length());
for (int i = i0; i < i1 && i >= 0; i = (isAll ? i + 1 : bs
.nextSetBit(i + 1)))
- sb.appendI(i).appendC('\t').appendF(
- type == VDW.USER ? vwr.userVdws[i] : Elements
- .getVanderwaalsMar(i, type) / 1000f).appendC('\t').append(
- Elements.elementSymbolFromNumber(i)).appendC('\n');
+ sb.appendI(i)
+ .appendC('\t')
+ .appendF(
+ type == VDW.USER ? vwr.userVdws[i] : Elements.getVanderwaalsMar(
+ i, type) / 1000f).appendC('\t')
+ .append(Elements.elementSymbolFromNumber(i)).appendC('\n');
return (bs == null ? sb.toString() : "\n DATA \"element_vdw\"\n"
+ sb.append(" end \"element_vdw\";\n\n").toString());
}
@@ -341,35 +311,39 @@
for (String name : dataValues.keySet()) {
if (name.indexOf("property_") == 0) {
Object[] obj = dataValues.get(name);
- if (obj.length > DATA_SAVE_IN_STATE
- && obj[DATA_SAVE_IN_STATE] == Boolean.FALSE)
+ // default for "save in state" is TRUE
+ if (obj.length > JmolDataManager.DATA_SAVE_IN_STATE
+ && !((Boolean) obj[JmolDataManager.DATA_SAVE_IN_STATE])
+ .booleanValue())
continue;
haveData = true;
- Object data = obj[1];
- if (data != null && ((Integer) obj[3]).intValue() == 1) {
+ Object data = obj[DATA_VALUE];
+ if (data != null
+ && getType(obj) == JmolDataManager.DATA_TYPE_AF) {
sc.getAtomicPropertyStateBuffer(sb, AtomCollection.TAINT_MAX,
- (BS) obj[2], name, (float[]) data);
+ (BS) obj[DATA_SELECTION], name, (float[]) data);
sb.append("\n");
} else {
- sb.append("\n").append(Escape.encapsulateData(name, data, 0));//j2s
issue?
+ // should not be here -- property_xxx is always float[]
+ sb.append("\n").append(
+ Escape.encapsulateData(name, data,
+ JmolDataManager.DATA_TYPE_UNKNOWN));//j2s issue?
}
- } else if (name.indexOf("data2d") == 0) {
- Object[] obj = dataValues.get(name);
- Object data = obj[1];
- if (data != null && ((Integer) obj[3]).intValue() == 2) {
- haveData = true;
- sb.append("\n").append(Escape.encapsulateData(name, data, 2));
- }
- } else if (name.indexOf("data3d") == 0) {
- Object[] obj = dataValues.get(name);
- Object data = obj[1];
- if (data != null && ((Integer) obj[3]).intValue() == 3) {
- haveData = true;
- sb.append("\n").append(Escape.encapsulateData(name, data, 3));
- }
+ continue;
}
+ int type = (name.indexOf("data2d") == 0 ? JmolDataManager.DATA_TYPE_AFF
+ : name.indexOf("data3d") == 0 ? JmolDataManager.DATA_TYPE_AFFF
+ : JmolDataManager.DATA_TYPE_UNKNOWN);
+ if (type == JmolDataManager.DATA_TYPE_UNKNOWN)
+ continue;
+ Object[] obj = dataValues.get(name);
+ Object data = obj[DATA_VALUE];
+ if (data != null && getType(obj) == type) {
+ haveData = true;
+ sb.append("\n").append(Escape.encapsulateData(name, data, type));
+ }
}
return haveData;
}
-
+
}
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-08-08 21:47:59 UTC
(rev 20686)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2015-08-10 00:15:14 UTC
(rev 20687)
@@ -51,8 +51,14 @@
TODO: curved arrows overextend and with width settings do not truncate shaft
properly
-Jmol.___JmolVersion="14.3.15_2015.08.08"
+Jmol.___JmolVersion="14.3.15_2015.08.09"
+bug fix: CML reader can fail (e.g. nsc244a.cml)
+
+code: refactoring of JmolDataManager
+
+JmolVersion="14.3.15_2015.08.08"
+
new feature: atom property "monomer" same as %g
new feature: atom property "seqcode" same as %r
new feature: load "test.pdb" from write property atomno temperature now
restores values for atomno and temperature for points on plot
Modified: trunk/Jmol/src/org/jmol/viewer/PropertyManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-08-08 21:47:59 UTC
(rev 20686)
+++ trunk/Jmol/src/org/jmol/viewer/PropertyManager.java 2015-08-10 00:15:14 UTC
(rev 20687)
@@ -49,6 +49,7 @@
import java.util.Properties;
import org.jmol.api.Interface;
+import org.jmol.api.JmolDataManager;
import org.jmol.api.JmolPropertyManager;
import org.jmol.java.BS;
import org.jmol.modelset.Atom;
@@ -621,7 +622,7 @@
case PROP_CONSOLE_TEXT:
return vwr.getProperty("DATA_API", "consoleText", null);
case PROP_DATA_INFO:
- return vwr.getData(myParam.toString());
+ return vwr.getDataObj(myParam.toString(), null,
JmolDataManager.DATA_TYPE_UNKNOWN);
case PROP_ERROR_MESSAGE:
return vwr.getErrorMessageUn();
case PROP_EVALUATE:
Modified: trunk/Jmol/src/org/jmol/viewer/StateCreator.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2015-08-08 21:47:59 UTC
(rev 20686)
+++ trunk/Jmol/src/org/jmol/viewer/StateCreator.java 2015-08-10 00:15:14 UTC
(rev 20687)
@@ -23,22 +23,22 @@
package org.jmol.viewer;
+import java.util.Arrays;
+import java.util.Date;
+import java.util.Hashtable;
+import java.util.Map;
+
import javajs.awt.Font;
import javajs.util.Lst;
+import javajs.util.P3;
import javajs.util.PT;
import javajs.util.SB;
-import java.util.Arrays;
-import java.util.Date;
-import java.util.Hashtable;
-
-import java.util.Map;
-
+import org.jmol.api.JmolDataManager;
import org.jmol.api.JmolModulationSet;
import org.jmol.api.JmolScriptFunction;
import org.jmol.api.SymmetryInterface;
import org.jmol.c.PAL;
-import org.jmol.c.STER;
import org.jmol.c.STR;
import org.jmol.c.VDW;
import org.jmol.java.BS;
@@ -66,14 +66,12 @@
import org.jmol.util.BSUtil;
import org.jmol.util.C;
import org.jmol.util.ColorEncoder;
+import org.jmol.util.Edge;
import org.jmol.util.Escape;
import org.jmol.util.GData;
-import org.jmol.util.Edge;
import org.jmol.util.Logger;
import org.jmol.util.Vibration;
-import javajs.util.P3;
-
/**
* StateCreator handles all aspects of working with the "state" as
* generally defined, including
@@ -479,11 +477,11 @@
String data = (String) vwr.ligandModels.get(key + "_data");
if (data != null)
cmds.append(" ").append(
- Escape.encapsulateData("ligand_" + key, data.trim() + "\n", 0));
+ Escape.encapsulateData("ligand_" + key, data.trim() + "\n",
JmolDataManager.DATA_TYPE_STRING));
data = (String) vwr.ligandModels.get(key + "_file");
if (data != null)
cmds.append(" ").append(
- Escape.encapsulateData("file_" + key, data.trim() + "\n", 0));
+ Escape.encapsulateData("file_" + key, data.trim() + "\n",
JmolDataManager.DATA_TYPE_STRING));
}
}
SB commands = new SB();
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-08-08 21:47:59 UTC (rev
20686)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2015-08-10 00:15:14 UTC (rev
20687)
@@ -2859,8 +2859,8 @@
}
public void setCurrentColorRange(String label) {
- float[] data = getDataFloat(label, null);
- BS bs = (data == null ? null : (BS) (getDataManager().getData(label))[2]);
+ float[] data = (float[]) getDataObj(label, null,
JmolDataManager.DATA_TYPE_AF);
+ BS bs = (data == null ? null : (BS) ((Object[])getDataObj(label, null,
JmolDataManager.DATA_TYPE_UNKNOWN))[2]);
if (bs != null && g.rangeSelected)
bs.and(bsA());
cm.setPropertyColorRangeData(data, bs);
@@ -2868,31 +2868,99 @@
private Object[] lastData;
- public void setData(String type, Object[] data, int arrayCount,
- int matchField, int matchFieldColumnCount, int field,
- int fieldColumnCount) {
- getDataManager().setData(type, lastData = data, arrayCount, ms.ac,
- matchField, matchFieldColumnCount, field, fieldColumnCount);
+ /**
+ * A general-purpose data storage method. Note that matchFieldCount and
+ * dataFieldCount should both be positive or both be negative.
+ *
+ * @param key
+ *
+ * a simple key name for the data, starting with "property_" if
user-defined
+ *
+ * @param data
+ *
+ * data[0] -- label
+ *
+ * data[1] -- string or float[] or float[][] or float[][][]
+ *
+ * data[2] -- selection bitset or int[] atomMap when field > 0
+ *
+ * data[3] -- arrayDepth
0(String),1(float[]),2(float[][]),3(float[][][]) or -1
+ * to indidate that it is set by data type
+ *
+ * data[4] -- Boolean.TRUE == saveInState
+ *
+ * @param dataType
+ *
+ * see JmolDataManager interface
+ *
+ * @param matchField
+ *
+ * if positive, data must match atomNo in this column
+ *
+ * if 0, no match column
+ *
+ * @param matchFieldColumnCount
+ * if positive, this number of characters in match column if 0,
+ * reference is to tokens, not characters
+ *
+ * @param dataField
+ *
+ * if positive, column containing the data
+ *
+ * if 0, values are a simple list; clear the data
+ *
+ * if Integer.MAX_VALUE, values are a simple list; don't clear the
data
+ *
+ * if Integer.MIN_VALUE, have one SINGLE data value for all selected
+ * atoms
+ *
+ * @param dataFieldColumnCount
+ *
+ * if positive, this number of characters in data column
+ *
+ * if 0, reference is to tokens, not characters
+ */
+ public void setData(String key, Object[] data, int dataType,
+ int matchField, int matchFieldColumnCount, int dataField,
+ int dataFieldColumnCount) {
+ getDataManager().setData(key, lastData = data, dataType, ms.ac,
+ matchField, matchFieldColumnCount, dataField, dataFieldColumnCount);
}
- public Object[] getData(String type) {
- return (type == null ? lastData : getDataManager().getData(type));
+ /**
+ * Retrieve a data object
+ *
+ * @param key
+ *
+ * @param bsSelected
+ *
+ * selected atoms; for DATA_AF only
+ *
+ * @param dataType
+ *
+ * see JmolDataManager interface
+ *
+ * @return data object
+ *
+ * data[0] -- label (same as key)
+ *
+ * data[1] -- string or float[] or float[][] or float[][][]
+ *
+ * data[2] -- selection bitset or int[] atomMap when field > 0
+ *
+ * data[3] -- arrayDepth
+ * 0(String),1(float[]),2(float[][]),3(float[][][]) or -1 to indicate
+ * that it is set by data type
+ *
+ * data[4] -- Boolean.TRUE == saveInState
+ */
+ public Object getDataObj(String key, BS bsSelected, int dataType) {
+ return (key == null && dataType == JmolDataManager.DATA_TYPE_LAST ?
lastData
+ : getDataManager().getData(key, bsSelected, dataType));
}
- public float[] getDataFloat(String label, BS bsSelected) {
- return getDataManager().getDataFloatA(label, bsSelected);
- }
-
- public float[][] getDataFloat2D(String label) {
- return getDataManager().getDataFloat2D(label);
- }
-
- public float[][][] getDataFloat3D(String label) {
- return getDataManager().getDataFloat3D(label);
- }
-
public float getDataFloatAt(String label, int atomIndex) {
- return getDataManager().getDataFloat(label, atomIndex);
+ return getDataManager().getDataFloatAt(label, atomIndex);
}
// boolean autoLoadOrientation() {
@@ -7519,7 +7587,7 @@
nY = Math.abs(nY);
float[][] fdata;
if (data == null) {
- fdata = getDataFloat2D(functionName);
+ fdata = (float[][]) getDataObj(functionName, null,
JmolDataManager.DATA_TYPE_AFF);
if (fdata != null)
return fdata;
data = "";
@@ -7544,7 +7612,7 @@
nZ = Math.abs(nZ);
float[][][] xyzdata;
if (data == null) {
- xyzdata = getDataFloat3D(functionName);
+ xyzdata = (float[][][]) getDataObj(functionName, null,
JmolDataManager.DATA_TYPE_AFF);
if (xyzdata != null)
return xyzdata;
data = "";
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