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[Jmol-commits] SF.net SVN: jmol: [8176] trunk/Jmol/src/org
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From: <ha...@us...> - 2007-08-31 21:45:29
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Revision: 8176
http://jmol.svn.sourceforge.net/jmol/?rev=8176&view=rev
Author: hansonr
Date: 2007-08-31 14:45:24 -0700 (Fri, 31 Aug 2007)
Log Message:
-----------
11.3.14
# bug fix: -g ignored on -n option, even if -w is present
# new feature: APPLICATION -q (quality) option
# adjustment: setting JPG default quality to 75, not 100
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/viewer/Eval.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/openscience/jmol/app/Jmol.java
Modified: trunk/Jmol/src/org/jmol/viewer/Eval.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-08-31 16:57:47 UTC (rev 8175)
+++ trunk/Jmol/src/org/jmol/viewer/Eval.java 2007-08-31 21:45:24 UTC (rev 8176)
@@ -7442,7 +7442,7 @@
} else {
len = -1;
if (quality <= 0)
- quality = 100;
+ quality = 75;
}
if (len == 0)
len = data.length();
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-31 16:57:47 UTC (rev 8175)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2007-08-31 21:45:24 UTC (rev 8176)
@@ -2,6 +2,11 @@
# bug fix: HDO not recognized as "water"
# bug fix: rotateSelected MOLECULAR not around {0 0 0}
+# bug fix: -g ignored on -n option, even if -w is present
+
+# new feature: APPLICATION -q (quality) option
+
+# adjustment: setting JPG default quality to 75, not 100
# new feature: {r,g,b} can be used in place of [r,g,b] for indicating color,
# allowing programmatic color definition:
#
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2007-08-31 16:57:47 UTC (rev 8175)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2007-08-31 21:45:24 UTC (rev 8176)
@@ -210,11 +210,13 @@
public void setAppletContext(String fullName, URL documentBase, URL codeBase,
String appletProxyOrCommandOptions) {
this.fullName = fullName = (fullName == null ? "" : fullName);
- this.appletDocumentBase = (documentBase == null ? "" : documentBase.toString());
- this.appletCodeBase = (codeBase == null ? "" : codeBase.toString());
+ this.appletDocumentBase = (documentBase == null ? "" : documentBase
+ .toString());
+ this.appletCodeBase = (codeBase == null ? "" : codeBase.toString());
int i = fullName.lastIndexOf("[");
this.htmlName = (i < 0 ? fullName : fullName.substring(0, i));
- this.syncId = (i < 0 ? "" : fullName.substring(i + 1, fullName.length() - 1));
+ this.syncId = (i < 0 ? "" : fullName
+ .substring(i + 1, fullName.length() - 1));
isApplet = (documentBase != null);
String str = appletProxyOrCommandOptions;
if (!isApplet) {
@@ -273,7 +275,7 @@
public String getExportDriverList() {
return (String) global.getParameter("exportDrivers");
}
-
+
private static int getJmolVersionInt() {
//11.9.999 --> 1109999
String s = JmolConstants.version;
@@ -520,9 +522,9 @@
}
boolean isInPosition(Point3f pt, float degrees) {
- return transformManager.isInPosition(pt, degrees);
+ return transformManager.isInPosition(pt, degrees);
}
-
+
void move(Vector3f dRot, float dZoom, Vector3f dTrans, float dSlab,
float floatSecondsTotal, int fps) {
//from Eval
@@ -1073,16 +1075,17 @@
public short getObjectMad(int objId) {
return (global.objStateOn[objId] ? global.objMad[objId] : 0);
}
-/*
- private void setRgbs(int rgorb, String color) {
- colorManager.setRgb(rgorb, Graphics3D.getArgbFromString(color));
- }
-
- int getRgb(int rgorb) {
- return colorManager.getRgb(rgorb);
- }
-*/
-
+
+ /*
+ private void setRgbs(int rgorb, String color) {
+ colorManager.setRgb(rgorb, Graphics3D.getArgbFromString(color));
+ }
+
+ int getRgb(int rgorb) {
+ return colorManager.getRgb(rgorb);
+ }
+ */
+
void setPropertyColorScheme(String scheme) {
Logger.info("Property color scheme: " + scheme);
global.propertyColorScheme = scheme;
@@ -1174,18 +1177,18 @@
}
public int[] getColorSchemeArray(String colorScheme) {
- return colorManager.getColorSchemeArray(colorScheme);
+ return colorManager.getColorSchemeArray(colorScheme);
}
-
+
public static void setUserScale(int[] scale) {
ColorManager.setUserScale(scale);
}
-
+
short getColixFromPalette(float val, float rangeMin, float rangeMax) {
//isosurface
return colorManager.getColixFromPalette(val, rangeMin, rangeMax);
}
-
+
Point3f getColorPointForPropertyValue(float val) {
//x = {atomno=3}.partialcharge.color
short colix = colorManager.getColixForPropertyValue(val);
@@ -1200,11 +1203,13 @@
void select(BitSet bs, boolean isQuiet) {
//Eval
selectionManager.select(bs, isQuiet);
- modelManager.setShapeSize(JmolConstants.SHAPE_STICKS, Integer.MAX_VALUE, null);
+ modelManager.setShapeSize(JmolConstants.SHAPE_STICKS, Integer.MAX_VALUE,
+ null);
}
void selectBonds(BitSet bs) {
- modelManager.setShapeSize(JmolConstants.SHAPE_STICKS, Integer.MAX_VALUE, bs);
+ modelManager
+ .setShapeSize(JmolConstants.SHAPE_STICKS, Integer.MAX_VALUE, bs);
}
BitSet getSelectedAtoms() {
@@ -1416,7 +1421,7 @@
}
private boolean openStringInline(String strModel, Hashtable htParams,
- boolean isMerge) {
+ boolean isMerge) {
//loadInline, openFile, openStringInline
if (!isMerge)
clear();
@@ -1428,7 +1433,7 @@
}
private void openStringsInline(String[] arrayModels, Hashtable htParams,
- boolean isMerge) {
+ boolean isMerge) {
//loadInline, openFile, openStringInline
if (!isMerge)
clear();
@@ -1623,8 +1628,8 @@
}
public String getFileAsString(String pathName) {
- return (pathName == null ? getCurrentFileAsString()
- : fileManager.getFileAsString(pathName));
+ return (pathName == null ? getCurrentFileAsString() : fileManager
+ .getFileAsString(pathName));
}
public String getFullPathName() {
@@ -1634,13 +1639,13 @@
public String getFileName() {
return fileManager.getFileName();
}
-
+
String[] getFileInfo() {
return fileManager.getFileInfo();
}
-
+
void setFileInfo(String[] fileInfo) {
- fileManager.setFileInfo(fileInfo);
+ fileManager.setFileInfo(fileInfo);
}
// ///////////////////////////////////////////////////////////////
@@ -1814,8 +1819,8 @@
}
public String getHybridizationAndAxes(int atomIndex, Vector3f z, Vector3f x,
- String lcaoType,
- boolean hybridizationCompatible) {
+ String lcaoType,
+ boolean hybridizationCompatible) {
return modelManager.getHybridizationAndAxes(atomIndex, z, x, lcaoType,
hybridizationCompatible);
}
@@ -1969,7 +1974,7 @@
public String getModelFileInfo() {
return modelManager.getModelFileInfo(getVisibleFramesBitSet());
}
-
+
public Hashtable getModelAuxiliaryInfo(int modelIndex) {
return modelManager.getModelAuxiliaryInfo(modelIndex);
}
@@ -2232,8 +2237,10 @@
+ getJmolVersion() + ";\n");
if (isApplet) {
StateManager.appendCmd(s, "# fullName = " + Escape.escape(fullName));
- StateManager.appendCmd(s, "# documentBase = " + Escape.escape(appletDocumentBase));
- StateManager.appendCmd(s, "# codeBase = " + Escape.escape(appletCodeBase));
+ StateManager.appendCmd(s, "# documentBase = "
+ + Escape.escape(appletDocumentBase));
+ StateManager
+ .appendCmd(s, "# codeBase = " + Escape.escape(appletCodeBase));
s.append("\n");
}
// window state
@@ -2264,7 +2271,8 @@
static Hashtable dataValues = new Hashtable();
- static void setData(String type, Object[] data, int atomCount, int matchField, int field) {
+ static void setData(String type, Object[] data, int atomCount,
+ int matchField, int field) {
//Eval
/*
* data[0] -- label
@@ -2683,7 +2691,7 @@
boolean isDataFrame(int modelIndex) {
return (modelIndex >= 0 && getModelAuxiliaryInfo(modelIndex, "jmolData") != null);
}
-
+
void setCurrentModelIndex(int modelIndex) {
//Eval
//initializeModel
@@ -2762,7 +2770,7 @@
private void setRefreshing(boolean TF) {
refreshing = TF;
}
-
+
boolean getRefreshing() {
return refreshing;
}
@@ -3165,7 +3173,8 @@
String strErrorMessage = eval.getErrorMessage();
if (isOK) {
statusManager.setStatusScriptStarted(++scriptIndex, strScript);
- eval.runEval(checkScriptOnly, !checkScriptOnly || fileOpenCheck, historyDisabled);
+ eval.runEval(checkScriptOnly, !checkScriptOnly || fileOpenCheck,
+ historyDisabled);
int msWalltime = eval.getExecutionWalltime();
strErrorMessage = eval.getErrorMessage();
statusManager.setStatusScriptTermination(strErrorMessage, msWalltime);
@@ -3199,12 +3208,12 @@
return null;
checking = true;
if (strScript.indexOf(")") == 0) // history disabled
- strScript = strScript.substring(1);
+ strScript = strScript.substring(1);
Object obj = eval.checkScriptSilent(strScript);
checking = false;
if (obj instanceof String)
return (String) obj;
- return null;
+ return null;
}
public boolean isScriptExecuting() {
@@ -3237,7 +3246,7 @@
statusManager.setCallbackFunction("language", language);
global.setParameterValue("language", GT.getLanguage());
}
-
+
private void setLoadFormat(String format) {
//Eval
global.loadFormat = format;
@@ -3358,12 +3367,13 @@
}
int n;
+
void togglePickingLabel(BitSet bs) {
//eval set toggleLabel (atomset)
loadShape(JmolConstants.SHAPE_LABELS);
setShapeSize(JmolConstants.SHAPE_LABELS, 0, null);
modelManager.setShapeProperty(JmolConstants.SHAPE_LABELS, "toggleLabel",
- null, bs);
+ null, bs);
refresh(0, "Viewer:");
}
@@ -3657,16 +3667,17 @@
global.setParameterValue("_modelNumber", s);
global.setParameterValue("_modelName", (modelIndex < 0 ? ""
: getModelName(modelIndex)));
- global.setParameterValue("_modelTitle", (modelIndex < 0 ? ""
- : modelManager.getModelTitle(modelIndex)));
- global.setParameterValue("_modelFile", (modelIndex < 0 ? ""
- : modelManager.getModelFile(modelIndex)));
+ global.setParameterValue("_modelTitle", (modelIndex < 0 ? "" : modelManager
+ .getModelTitle(modelIndex)));
+ global.setParameterValue("_modelFile", (modelIndex < 0 ? "" : modelManager
+ .getModelFile(modelIndex)));
s = statusManager.getCallbackScript("animframecallback");
if (s != null)
evalStringQuiet(s, true);
else
- statusManager.setStatusFrameChanged(frameNo, fileNo, modelNo, (repaintManager.animationDirection < 0 ? -firstNo : firstNo),
+ statusManager.setStatusFrameChanged(frameNo, fileNo, modelNo,
+ (repaintManager.animationDirection < 0 ? -firstNo : firstNo),
(repaintManager.currentDirection < 0 ? -lastNo : lastNo));
}
@@ -3818,26 +3829,25 @@
while (true) {
///11.1.31//
/* didn't work
- if (key.equalsIgnoreCase("rgbRed")) {
- setRgbs(0, value);
- break;
- }
- if (key.equalsIgnoreCase("rgbGreen")) {
- setRgbs(1, value);
- break;
- }
- if (key.equalsIgnoreCase("rgbBlue")) {
- setRgbs(2, value);
- break;
- }
- */
+ if (key.equalsIgnoreCase("rgbRed")) {
+ setRgbs(0, value);
+ break;
+ }
+ if (key.equalsIgnoreCase("rgbGreen")) {
+ setRgbs(1, value);
+ break;
+ }
+ if (key.equalsIgnoreCase("rgbBlue")) {
+ setRgbs(2, value);
+ break;
+ }
+ */
///11.1.30//
if (key.equalsIgnoreCase("language")) {
setLanguage(value); //fr cs en none, etc.
return;
}
-
-
+
///11.1.22//
if (key.equalsIgnoreCase("loadFormat")) {
@@ -4090,14 +4100,13 @@
private void setIntProperty(String key, int value, boolean defineNew) {
while (true) {
-
+
///11.1.31//
-
+
if (key.equalsIgnoreCase("propertyDataField")) {
break;
}
-
///11.1///
if (key.equalsIgnoreCase("strandCount")) {
@@ -4741,7 +4750,7 @@
|| getAxesMode() != JmolConstants.AXES_MODE_UNITCELL ? null
: (Point3f[]) getShapeProperty(JmolConstants.SHAPE_AXES, "axisPoints"));
}
-
+
public float getAxesScale() {
return global.axesScale;
}
@@ -5618,7 +5627,8 @@
modelManager.invertSelected(pt, plane, selectionManager.bsSelection);
}
- void rotateSelected(Matrix3f mNew, Matrix3f matrixRotate, boolean fullMolecule, boolean isInternal) {
+ void rotateSelected(Matrix3f mNew, Matrix3f matrixRotate,
+ boolean fullMolecule, boolean isInternal) {
modelManager.rotateSelected(mNew, matrixRotate,
selectionManager.bsSelection, fullMolecule, isInternal);
}
@@ -5664,7 +5674,7 @@
}
void getHelp(String what) {
- if (what.length() > 0 && what.indexOf("?") != 0
+ if (what.length() > 0 && what.indexOf("?") != 0
&& global.helpPath.indexOf("?") < 0)
what = "?search=" + what;
showUrl(global.helpPath + what);
@@ -5721,33 +5731,47 @@
// image export
// ///////////////////////////////////////////////////////////////
- void createImage(String type_name) { // or script now
+ private void createImage(String type_name) { // or script now
+ int quality, width, height;
if (type_name == null)
return;
if (type_name.length() == 0)
type_name = "JPG:jmol.jpg";
+ if (type_name.indexOf(":") < 0)
+ type_name += ":jmol.jpg";
int i = type_name.indexOf(":");
- if (i < 0) {
- i = type_name.length();
- type_name += ":jmol.jpg";
- }
String type = type_name.substring(0, i);
String file = type_name.substring(i + 1);
- createImage(file, type, 100);
+ String swidth = "-1";
+ String sheight = "-1";
+ String squality = "75";
+ i = file.indexOf('\t');
+ if (i > 0) {
+ swidth = file.substring(i + 1);
+ file = file.substring(0, i);
+ }
+ i = swidth.indexOf('\t');
+ if (i > 0) {
+ sheight = swidth.substring(i + 1);
+ swidth = swidth.substring(0, i);
+ }
+ i = sheight.indexOf('\t');
+ if (i > 0) {
+ squality = sheight.substring(i + 1);
+ sheight = sheight.substring(0, i);
+ }
+ try {
+ width = Integer.parseInt(swidth);
+ height = Integer.parseInt(sheight);
+ quality = Integer.parseInt(squality);
+ createImage(file, type, quality, width, height);
+ } catch (Exception e) {
+ System.out.println("error processing write request: " + type_name);
+ }
}
- /**
- *
- * @param file filename or null for clipboard
- * @param type_text = data type if quality < Integer.MAX_VALUE; otherwise text
- * @param quality up to 100 for JPG quality; Integer.MAX_VALUE for text
- */
- public void createImage(String file, String type_text, int quality) {
- createImage(file, type_text, quality, -1, -1);
- }
-
- public void createImage(String file, String type_text, int quality, int width,
- int height) {
+ public void createImage(String file, String type_text, int quality,
+ int width, int height) {
int saveWidth = dimScreen.width;
int saveHeight = dimScreen.height;
if (width > 0 && height > 0)
@@ -5766,7 +5790,7 @@
boolean isAll = ("*".equals(applet));
boolean allButMe = (">".equals(applet));
boolean disableSend = ("~".equals(applet));
- boolean justMe = disableSend || (".".equals(applet));
+ boolean justMe = disableSend || (".".equals(applet));
//null same as ">" -- "all others"
if (justMe) {
} else {
@@ -5799,19 +5823,19 @@
statusManager.setSyncDriver(StatusManager.SYNC_DISABLE);
evalStringQuiet(script, true);
}
-
+
void setSyncDriver(int mode) {
- statusManager.setSyncDriver(mode);
+ statusManager.setSyncDriver(mode);
}
-
+
public float[] getPartialCharges() {
return modelManager.getPartialCharges();
}
void setProteinType(byte iType, BitSet bs) {
- modelManager.setProteinType(bs == null ? selectionManager.bsSelection : bs, iType);
+ modelManager.setProteinType(bs == null ? selectionManager.bsSelection : bs,
+ iType);
}
-
/*
void debugStack(String msg) {
Modified: trunk/Jmol/src/org/openscience/jmol/app/Jmol.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/Jmol.java 2007-08-31 16:57:47 UTC (rev 8175)
+++ trunk/Jmol/src/org/openscience/jmol/app/Jmol.java 2007-08-31 21:45:24 UTC (rev 8176)
@@ -495,6 +495,13 @@
OptionBuilder.hasArg();
options.addOption(OptionBuilder.create("g"));
+ OptionBuilder.withLongOpt("quality");
+ // OptionBuilder.withDescription(GT._("overall window width x height, e.g. {0}", "-g512x616"));
+ OptionBuilder.withDescription(GT._("JPG image quality (1-100)"));
+ OptionBuilder.withValueSeparator();
+ OptionBuilder.hasArg();
+ options.addOption(OptionBuilder.create("q"));
+
OptionBuilder.withLongOpt("write");
OptionBuilder.withDescription(GT._("{0} or {1}:filename", new Object[] {
"CLIP", "JPG|JPG64|PNG|PPM" }));
@@ -586,11 +593,10 @@
if (line.hasOption("x")) {
commandOptions += "-x";
}
-
+ String imageType_name = null;
//write image to clipboard or image file
if (line.hasOption("w")) {
- String type_name = line.getOptionValue("w");
- commandOptions += "-w\1" + type_name + "\1";
+ imageType_name = line.getOptionValue("w");
}
try {
@@ -629,16 +635,30 @@
//note -- the first time this is run after changes it will not work
//because there is a bootstrap problem.
+ int width = -1;
+ int height = -1;
+ int quality = 75;
//INNER frame dimensions
- if (line.hasOption("g") && haveDisplay.booleanValue()) {
+ if (line.hasOption("g")) {
String geometry = line.getOptionValue("g");
int indexX = geometry.indexOf('x');
if (indexX > 0) {
- startupWidth = parseInt(geometry.substring(0, indexX)) + border.x;
- startupHeight = parseInt(geometry.substring(indexX + 1)) + border.y;
+ width = parseInt(geometry.substring(0, indexX));
+ height = parseInt(geometry.substring(indexX + 1));
//System.out.println("setting geometry to " + geometry + " " + border + " " + startupWidth + startupHeight);
}
+ if (haveDisplay.booleanValue()) {
+ startupWidth = width + border.x;
+ startupHeight = height + border.y;
+ }
}
+
+ if (line.hasOption("q"))
+ quality = parseInt(line.getOptionValue("q"));
+
+ if (imageType_name != null)
+ commandOptions += "-w\1" + imageType_name + "\t"+width+"\t"+height + "\t" + quality + "\1";
+
if (startupWidth <= 0 || startupHeight <= 0) {
startupWidth = 500 + border.x;
startupHeight = 500 + border.y;
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