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[Jmol-commits] SF.net SVN: jmol:[12896] trunk/Jmol/src/org
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From: <ha...@us...> - 2010-04-20 12:25:28
|
Revision: 12896
http://jmol.svn.sourceforge.net/jmol/?rev=12896&view=rev
Author: hansonr
Date: 2010-04-20 12:25:20 +0000 (Tue, 20 Apr 2010)
Log Message:
-----------
version=12.0.RC7_dev
# new feature: drag-and-drop defaults for map files and PDB files
# bug fix: VRML exporter fails to remove duplicate spheres if not same color
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
trunk/Jmol/src/org/jmol/export/JmolFileDropper.java
trunk/Jmol/src/org/jmol/export/_VrmlExporter.java
trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceFileReader.java
trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/ScriptFunction.java
trunk/Jmol/src/org/jmol/shape/MeshCollection.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/Viewer.java
trunk/Jmol/src/org/openscience/jmol/app/JmolApp.java
Added Paths:
-----------
trunk/Jmol/src/org/jmol/util/SurfaceFileTyper.java
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2010-04-19 13:09:07 UTC (rev 12895)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/AtomSetCollectionReader.java 2010-04-20 12:25:20 UTC (rev 12896)
@@ -684,12 +684,12 @@
String groups = (String) htSite.get("groups");
if (groups.length() == 0)
continue;
- addJmolScript("@site_" + name + " " + groups);
+ addSiteScript("@site_" + name + " " + groups);
//addJmolScript("@" + seqNum + " " + groups);
- addJmolScript("site_" + name + " = \"" + groups + "\".split(\",\")");
+ addSiteScript("site_" + name + " = \"" + groups + "\".split(\",\")");
sites += (sites == "" ? "" : ",") + "site_" + name;
}
- addJmolScript("site_list = \"" + sites + "\".split(\",\")");
+ addSiteScript("site_list = \"" + sites + "\".split(\",\")");
}
public void applySymmetryAndSetTrajectory() throws Exception {
@@ -946,6 +946,17 @@
previousScript);
}
+ private String siteScript;
+ protected void addSiteScript(String script) {
+ if (siteScript == null)
+ siteScript = "";
+ else if (!siteScript.endsWith(";"))
+ siteScript += ";";
+ siteScript += script;
+ atomSetCollection.setAtomSetCollectionAuxiliaryInfo("sitescript",
+ siteScript);
+ }
+
public String readLine() throws Exception {
prevline = line;
line = reader.readLine();
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-04-19 13:09:07 UTC (rev 12895)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2010-04-20 12:25:20 UTC (rev 12896)
@@ -913,7 +913,7 @@
private final static String[] pdbLineStartRecords = {
"Pdb", "HEADER", "OBSLTE", "TITLE ", "CAVEAT", "COMPND", "SOURCE", "KEYWDS",
- "EXPDTA", "AUTHOR", "REVDAT", "SPRSDE", "JRNL ", "REMARK",
+ "EXPDTA", "AUTHOR", "REVDAT", "SPRSDE", "JRNL ", "REMARK ",
"DBREF ", "SEQADV", "SEQRES", "MODRES",
"HELIX ", "SHEET ", "TURN ",
"CRYST1", "ORIGX1", "ORIGX2", "ORIGX3", "SCALE1", "SCALE2", "SCALE3",
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java 2010-04-19 13:09:07 UTC (rev 12895)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java 2010-04-20 12:25:20 UTC (rev 12896)
@@ -378,16 +378,10 @@
}
public String getFileTypeName(Object atomSetCollectionOrReader) {
- return staticGetFileTypeName(atomSetCollectionOrReader);
- }
-
- private static String staticGetFileTypeName(Object atomSetCollectionOrReader) {
- if (atomSetCollectionOrReader == null)
- return null;
- if (atomSetCollectionOrReader instanceof BufferedReader)
- return Resolver.getFileType((BufferedReader)atomSetCollectionOrReader);
if (atomSetCollectionOrReader instanceof AtomSetCollection)
return ((AtomSetCollection)atomSetCollectionOrReader).getFileTypeName();
+ if (atomSetCollectionOrReader instanceof BufferedReader)
+ return Resolver.getFileType((BufferedReader)atomSetCollectionOrReader);
return null;
}
Modified: trunk/Jmol/src/org/jmol/export/JmolFileDropper.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/JmolFileDropper.java 2010-04-19 13:09:07 UTC (rev 12895)
+++ trunk/Jmol/src/org/jmol/export/JmolFileDropper.java 2010-04-20 12:25:20 UTC (rev 12896)
@@ -89,10 +89,7 @@
private void loadFile(String fname) {
if (fname.indexOf("://") < 0)
fname = (fname.startsWith("/") ? "file://" : "file:///") + fname;
- if (fname.endsWith(".jvxl") || fname.endsWith(".xjvxl"))
- viewer.script("isosurface " + Escape.escape(fname));
- else
- viewer.script("load " + Escape.escape(fname));
+ viewer.openFileAsynchronously(fname);
}
private void loadFiles(List fileList) {
Modified: trunk/Jmol/src/org/jmol/export/_VrmlExporter.java
===================================================================
--- trunk/Jmol/src/org/jmol/export/_VrmlExporter.java 2010-04-19 13:09:07 UTC (rev 12895)
+++ trunk/Jmol/src/org/jmol/export/_VrmlExporter.java 2010-04-20 12:25:20 UTC (rev 12896)
@@ -350,8 +350,9 @@
Hashtable htSpheresRendered = new Hashtable();
protected void outputSphere(Point3f center, float radius, short colix) {
- String child = useTable.getDef("S" + colix + "_" + (int) (radius * 100));
- String check = child + " " + center;
+ int iRad = (int) (radius * 100);
+ String child = useTable.getDef("S" + colix + "_" + iRad);
+ String check = round(center) + " " + iRad;
if (htSpheresRendered.get(check) != null)
return;
htSpheresRendered.put(check, Boolean.TRUE);
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java 2010-04-19 13:09:07 UTC (rev 12895)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/PmeshReader.java 2010-04-20 12:25:20 UTC (rev 12896)
@@ -30,6 +30,7 @@
import org.jmol.jvxl.data.JvxlCoder;
import org.jmol.util.BinaryDocument;
import org.jmol.util.Logger;
+import org.jmol.util.SurfaceFileTyper;
/*
*
@@ -87,7 +88,7 @@
private int nPolygons;
private boolean isBinary;
- final static String PMESH_BINARY_MAGIC_NUMBER = "PM" + '\1' + '\0';
+ final static String PMESH_BINARY_MAGIC_NUMBER = SurfaceFileTyper.PMESH_BINARY_MAGIC_NUMBER;
String pmeshError;
PmeshReader(SurfaceGenerator sg, String fileName, BufferedReader br) {
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceFileReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceFileReader.java 2010-04-19 13:09:07 UTC (rev 12895)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceFileReader.java 2010-04-20 12:25:20 UTC (rev 12896)
@@ -66,73 +66,6 @@
binarydoc.close();
}
- static String determineFileType(BufferedReader bufferedReader) {
- // JVXL should be on the FIRST line of the file, but it may be
- // after comments or missing.
-
- // Apbs, Jvxl, or Cube, also efvet
-
- String line;
- LimitedLineReader br = new LimitedLineReader(bufferedReader, 16000);
- //sure bets, but not REQUIRED:
- if ((line = br.info()).length() == 0)
- return "UNKNOWN";
- if (line.indexOf("<jvxl") >= 0 && line.indexOf("<?xml") >= 0)
- return "JvxlXML";
- if (line.indexOf("#JVXL+") >= 0)
- return "Jvxl+";
- if (line.indexOf("#JVXL") >= 0)
- return "Jvxl";
- if (line.indexOf("&plot") == 0)
- return "Jaguar";
- if (line.indexOf("MAP ") == 208)
- return "MRC" + (line.charAt(67) == '\0' ? "L" : "B");
- if (line.indexOf("<efvet ") >= 0)
- return "Efvet";
- if (line.indexOf(PmeshReader.PMESH_BINARY_MAGIC_NUMBER) == 0)
- return "Pmesh";
- if ("\n\r".indexOf(line.charAt(0)) >= 0 && line.indexOf("ZYX") >= 0)
- return "Xplor";
- if (line.length() > 37 && line.charAt(36) == 0 && line.charAt(37) == 100)
- return "DSN6B";
- if (line.length() > 37 && line.charAt(37) == 100 && line.charAt(36) == 0)
- return "DSN6L";
-
- // Apbs, Jvxl, or Cube, maybe formatted Plt
-
- line = br.readNonCommentLine();
- if (line.indexOf("object 1 class gridpositions counts") == 0)
- return "Apbs";
-
- String[] tokens = Parser.getTokens(line);
- line = br.readNonCommentLine();// second line
- if (tokens.length == 2
- && Parser.parseInt(tokens[0]) == 3
- && Parser.parseInt(tokens[1])!= Integer.MIN_VALUE) {
- tokens = Parser.getTokens(line);
- if (tokens.length == 3
- && Parser.parseInt(tokens[0])!= Integer.MIN_VALUE
- && Parser.parseInt(tokens[1])!= Integer.MIN_VALUE
- && Parser.parseInt(tokens[2])!= Integer.MIN_VALUE)
- return "PltFormatted";
- }
- line = br.readNonCommentLine(); // third line
- //next line should be the atom line
- int nAtoms = Parser.parseInt(line);
- if (nAtoms == Integer.MIN_VALUE)
- return (line.indexOf("+") == 0 ? "Jvxl+" : "UNKNOWN");
- if (nAtoms >= 0)
- return "Cube"; //Can't be a Jvxl file
- nAtoms = -nAtoms;
- for (int i = 4 + nAtoms; --i >=0;)
- if ((line = br.readNonCommentLine()) == null)
- return "UNKNOWN";
- int nSurfaces = Parser.parseInt(line);
- if (nSurfaces == Integer.MIN_VALUE)
- return "UNKNOWN";
- return (nSurfaces < 0 ? "Jvxl" : "Cube"); //Final test looks at surface definition line
- }
-
void discardTempData(boolean discardAll) {
closeReader();
super.discardTempData(discardAll);
@@ -203,43 +136,3 @@
}
}
-class LimitedLineReader {
- //from Resolver
- private char[] buf;
- private int cchBuf;
- private int ichCurrent;
-
- LimitedLineReader(BufferedReader bufferedReader, int readLimit) {
- buf = new char[readLimit];
- try {
- bufferedReader.mark(readLimit);
- cchBuf = bufferedReader.read(buf);
- ichCurrent = 0;
- bufferedReader.reset();
- } catch (Exception e) {
- }
- }
-
- protected String info() {
- return new String(buf);
- }
-
- protected String readNonCommentLine() {
- while (ichCurrent < cchBuf) {
- int ichBeginningOfLine = ichCurrent;
- char ch = 0;
- while (ichCurrent < cchBuf &&
- (ch = buf[ichCurrent++]) != '\r' && ch != '\n') {
- }
- int cchLine = ichCurrent - ichBeginningOfLine;
- if (ch == '\r' && ichCurrent < cchBuf && buf[ichCurrent] == '\n')
- ++ichCurrent;
- if (buf[ichBeginningOfLine] == '#') // flush comment lines;
- continue;
- StringBuffer sb = new StringBuffer(cchLine);
- sb.append(buf, ichBeginningOfLine, cchLine);
- return sb.toString();
- }
- return "";
- }
-}
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java 2010-04-19 13:09:07 UTC (rev 12895)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceGenerator.java 2010-04-20 12:25:20 UTC (rev 12896)
@@ -1086,7 +1086,9 @@
}
BufferedReader br = (BufferedReader) value;
if (fileType == null)
- fileType = SurfaceFileReader.determineFileType(br);
+ fileType = SurfaceFileTyper.determineSurfaceFileType(br);
+ if (fileType == null)
+ fileType = "UNKNOWN";
Logger.info("data file type was determined to be " + fileType);
if (fileType.equals("Jvxl+"))
return new JvxlReader(this, br);
Modified: trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java 2010-04-19 13:09:07 UTC (rev 12895)
+++ trunk/Jmol/src/org/jmol/jvxl/readers/SurfaceReader.java 2010-04-20 12:25:20 UTC (rev 12896)
@@ -323,8 +323,8 @@
if (!readAndSetVolumeParameters())
return false;
if (!justForPlane && params.sigma != Float.MAX_VALUE && !allowSigma) {
- Logger.error("Reader does not support SIGMA option");
- return false;
+ Logger.error("Reader does not support SIGMA option -- using cutoff 1.6");
+ params.cutoff = 1.6f;
}
nPointsX = voxelCounts[0];
nPointsY = voxelCounts[1];
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-19 13:09:07 UTC (rev 12895)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2010-04-20 12:25:20 UTC (rev 12896)
@@ -67,6 +67,7 @@
import org.jmol.util.Parser;
import org.jmol.util.Point3fi;
import org.jmol.util.Quaternion;
+import org.jmol.util.SurfaceFileTyper;
import org.jmol.util.TextFormat;
import org.jmol.modelset.TickInfo;
import org.jmol.viewer.ActionManager;
@@ -1937,6 +1938,8 @@
BitSetUtil.deleteBits((BitSet) value, bsDeleted);
}
}
+
+ //Hashtable thisCommandVariables;
/**
* provides support for @x and @{....} in statements. The compiler passes on
@@ -1950,6 +1953,7 @@
private boolean setStatement(int pc) throws ScriptException {
statement = aatoken[pc];
statementLength = statement.length;
+ //thisCommandVariables = null;
if (statementLength == 0)
return true;
Token[] fixed;
@@ -1969,6 +1973,7 @@
fixed[0] = statement[0];
boolean isExpression = false;
int j = 1;
+ //thisCommandVariables = new Hashtable();
for (i = 1; i < statementLength; i++) {
if (statement[i] == null)
continue;
@@ -1986,8 +1991,10 @@
i = iToken;
ScriptVariable vt = (ScriptVariable) val.elementAt(0);
v = (vt.tok == Token.list ? vt : ScriptVariable.oValue(vt));
+// thisCommandVariables.put("v", v);
} else {
v = getParameter(var, false);
+// thisCommandVariables.put(var, v);
}
tok = tokAt(0);
boolean forceString = (Token.tokAttr(tok, Token.implicitStringCommand)
@@ -4801,7 +4808,7 @@
invertSelected();
break;
case Token.javascript:
- script(Token.javascript);
+ script(Token.javascript, null);
break;
case Token.load:
load();
@@ -4868,7 +4875,7 @@
set();
break;
case Token.script:
- script(Token.script);
+ script(Token.script, null);
break;
case Token.select:
select(1);
@@ -7218,16 +7225,14 @@
} else {
modelName = parameterAsString(i);
tok = tokAt(i);
- /* I have no idea what this was about.
- if (modelName.equalsIgnoreCase("data")) {
- modelName = stringParameter(++i);
- if (!isSyntaxCheck)
- htParams.put("parameterData", viewer.getFileAsString(modelName));
- loadScript.append(" data / *file* /").append(Escape.escape(modelName));
- tok = tokAt(++i);
- modelName = parameterAsString(i);
- }
- */
+ /*
+ * I have no idea what this was about. if
+ * (modelName.equalsIgnoreCase("data")) { modelName =
+ * stringParameter(++i); if (!isSyntaxCheck) htParams.put("parameterData",
+ * viewer.getFileAsString(modelName));
+ * loadScript.append(" data / *file* /").append(Escape.escape(modelName));
+ * tok = tokAt(++i); modelName = parameterAsString(i); }
+ */
if (tok == Token.identifier || modelName.equalsIgnoreCase("fileset")) {
if (modelName.equals("menu")) {
String m = parameterAsString(checkLast(2));
@@ -7253,8 +7258,9 @@
}
if (isAppend
&& ((filename = optParameterAsString(i))
- .equalsIgnoreCase("trajectory") || filename
- .equalsIgnoreCase("models") || filename.equalsIgnoreCase("inline"))) {
+ .equalsIgnoreCase("trajectory")
+ || filename.equalsIgnoreCase("models") || filename
+ .equalsIgnoreCase("inline"))) {
modelName = filename;
loadScript.append(" " + modelName);
i++;
@@ -7280,7 +7286,7 @@
htParams.put("firstLastStep", new int[] { 0, -1, 1 });
}
}
- } else if (modelName.equalsIgnoreCase("inline")){
+ } else if (modelName.equalsIgnoreCase("inline")) {
} else {
modelName = "fileset";
}
@@ -7538,11 +7544,19 @@
// but there could state problems here because then we don't have the
// option to save load options with that... Hmm.
if (errMsg != null && !isCmdLine_c_or_C_Option) {
- if (errMsg.indexOf("NOTE: file recognized as a script file:") == 0) {
- viewer.addLoadScript("-");
- errMsg = TextFormat.trim(errMsg, "\n");
- runScript("script \"" + errMsg.substring(40) + "\"");
- return;
+ if (statementLength == 2) {
+ if (errMsg.indexOf("NOTE: file recognized as a script file:") == 0) {
+ viewer.addLoadScript("-");
+ script(0, filename);
+ return;
+ }
+ String surfaceType = SurfaceFileTyper.determineSurfaceFileType(viewer
+ .getBufferedInputStream(filename));
+ if (surfaceType != null) {
+ viewer.addLoadScript("-");
+ runScript("isosurface " + Escape.escape(filename));
+ return;
+ }
}
evalError(errMsg, null);
}
@@ -7552,23 +7566,28 @@
}
if (logMessages)
scriptStatusOrBuffer("Successfully loaded:" + modelName);
- String defaultScript = viewer.getDefaultLoadScript();
+ String script = viewer.getDefaultLoadScript();
String msg = "";
- if (defaultScript.length() > 0)
- msg += "\nUsing defaultLoadScript: " + defaultScript;
- String script = (String) viewer.getModelSetAuxiliaryInfo("jmolscript");
+ if (script.length() > 0)
+ msg += "\nUsing defaultLoadScript: " + script;
+ String embeddedScript = (String) viewer.getModelSetAuxiliaryInfo("jmolscript");
viewer.getModelSetAuxiliaryInfo().remove("jmolscript");
- if (script != null && viewer.getAllowEmbeddedScripts()) {
- msg += "\nAdding embedded #jmolscript: " + script;
- defaultScript += ";" + script;
- defaultScript = "allowEmbeddedScripts = false;" + defaultScript
+ if (embeddedScript != null && viewer.getAllowEmbeddedScripts()) {
+ msg += "\nAdding embedded #jmolscript: " + embeddedScript;
+ script += ";" + embeddedScript;
+ viewer.setStringProperty("_loadScript", script);
+ script = "allowEmbeddedScripts = false;" + script
+ ";allowEmbeddedScripts = true;";
}
if (msg.length() > 0)
Logger.info(msg);
- if (defaultScript.length() > 0 && !isCmdLine_c_or_C_Option)
+ String siteScript = (String) viewer.getModelSetAuxiliaryInfo("sitescript");
+ viewer.getModelSetAuxiliaryInfo().remove("sitescript");
+ if (siteScript != null)
+ script = siteScript + ";" + script;
+ if (script.length() > 0 && !isCmdLine_c_or_C_Option)
// NOT checking embedded scripts in some cases
- runScript(defaultScript);
+ runScript(script);
}
private String getFullPathName() throws ScriptException {
@@ -8378,7 +8397,7 @@
data) ? (Vector3f) data[2] : null);
}
- private void script(int tok) throws ScriptException {
+ private void script(int tok, String filename) throws ScriptException {
boolean loadCheck = true;
boolean isCheck = false;
boolean doStep = false;
@@ -8388,7 +8407,6 @@
int pcEnd = 0;
int i = 2;
String theScript = parameterAsString(1);
- String filename = null;
String localPath = null;
String remotePath = null;
String scriptPath = null;
@@ -8398,78 +8416,83 @@
viewer.jsEval(theScript);
return;
}
- tok = tokAt(1);
- if (tok != Token.string)
- error(ERROR_filenameExpected);
- filename = parameterAsString(1);
- if (filename.equalsIgnoreCase("applet")) {
- // script APPLET x "....."
- String appID = parameterAsString(2);
- theScript = parameterExpression(3, 0, "_script", false).toString();
- checkLast(iToken);
- if (isSyntaxCheck)
- return;
- if (appID.length() == 0 || appID.equals("all"))
- appID = "*";
- if (!appID.equals(".")) {
- viewer.jsEval(appID + "\1" + theScript);
- if (!appID.equals("*"))
+ if (filename == null) {
+ tok = tokAt(1);
+ if (tok != Token.string)
+ error(ERROR_filenameExpected);
+ filename = parameterAsString(1);
+ if (filename.equalsIgnoreCase("applet")) {
+ // script APPLET x "....."
+ String appID = parameterAsString(2);
+ theScript = parameterExpression(3, 0, "_script", false).toString();
+ checkLast(iToken);
+ if (isSyntaxCheck)
return;
- }
- } else {
- theScript = null;
- tok = tokAt(statementLength - 1);
- doStep = (tok == Token.step);
- if (filename.equalsIgnoreCase("inline")) {
- theScript = parameterExpression(2, (doStep ? statementLength - 1 : 0),
- "_script", false).toString();
- i = iToken + 1;
- }
- while (filename.equalsIgnoreCase("localPath")
- || filename.equalsIgnoreCase("remotePath")
- || filename.equalsIgnoreCase("scriptPath")) {
- if (filename.equalsIgnoreCase("localPath"))
- localPath = parameterAsString(i++);
- else if (filename.equalsIgnoreCase("scriptPath"))
- scriptPath = parameterAsString(i++);
- else
- remotePath = parameterAsString(i++);
- filename = parameterAsString(i++);
- }
- if ((tok = tokAt(i)) == Token.check) {
- isCheck = true;
- tok = tokAt(++i);
- }
- if (tok == Token.noload) {
- loadCheck = false;
- tok = tokAt(++i);
- }
- if (tok == Token.line || tok == Token.lines) {
- i++;
- lineEnd = lineNumber = Math.max(intParameter(i++), 0);
- if (checkToken(i)) {
- if (getToken(i).tok == Token.minus)
- lineEnd = (checkToken(++i) ? intParameter(i++) : 0);
- else
- lineEnd = -intParameter(i++);
- if (lineEnd <= 0)
- error(ERROR_invalidArgument);
+ if (appID.length() == 0 || appID.equals("all"))
+ appID = "*";
+ if (!appID.equals(".")) {
+ viewer.jsEval(appID + "\1" + theScript);
+ if (!appID.equals("*"))
+ return;
}
- } else if (tok == Token.command || tok == Token.commands) {
- i++;
- pc = Math.max(intParameter(i++) - 1, 0);
- pcEnd = pc + 1;
- if (checkToken(i)) {
- if (getToken(i).tok == Token.minus)
- pcEnd = (checkToken(++i) ? intParameter(i++) : 0);
+ } else {
+ theScript = null;
+ tok = tokAt(statementLength - 1);
+ doStep = (tok == Token.step);
+ if (filename.equalsIgnoreCase("inline")) {
+ theScript = parameterExpression(2,
+ (doStep ? statementLength - 1 : 0), "_script", false).toString();
+ i = iToken + 1;
+ }
+ while (filename.equalsIgnoreCase("localPath")
+ || filename.equalsIgnoreCase("remotePath")
+ || filename.equalsIgnoreCase("scriptPath")) {
+ if (filename.equalsIgnoreCase("localPath"))
+ localPath = parameterAsString(i++);
+ else if (filename.equalsIgnoreCase("scriptPath"))
+ scriptPath = parameterAsString(i++);
else
- pcEnd = -intParameter(i++);
- if (pcEnd <= 0)
- error(ERROR_invalidArgument);
+ remotePath = parameterAsString(i++);
+ filename = parameterAsString(i++);
}
+ if ((tok = tokAt(i)) == Token.check) {
+ isCheck = true;
+ tok = tokAt(++i);
+ }
+ if (tok == Token.noload) {
+ loadCheck = false;
+ tok = tokAt(++i);
+ }
+ if (tok == Token.line || tok == Token.lines) {
+ i++;
+ lineEnd = lineNumber = Math.max(intParameter(i++), 0);
+ if (checkToken(i)) {
+ if (getToken(i).tok == Token.minus)
+ lineEnd = (checkToken(++i) ? intParameter(i++) : 0);
+ else
+ lineEnd = -intParameter(i++);
+ if (lineEnd <= 0)
+ error(ERROR_invalidArgument);
+ }
+ } else if (tok == Token.command || tok == Token.commands) {
+ i++;
+ pc = Math.max(intParameter(i++) - 1, 0);
+ pcEnd = pc + 1;
+ if (checkToken(i)) {
+ if (getToken(i).tok == Token.minus)
+ pcEnd = (checkToken(++i) ? intParameter(i++) : 0);
+ else
+ pcEnd = -intParameter(i++);
+ if (pcEnd <= 0)
+ error(ERROR_invalidArgument);
+ }
+ }
+ checkLength(doStep ? i + 1 : i);
}
- checkLength(doStep ? i + 1 : i);
}
+
+ // processing
+
if (isSyntaxCheck && !isCmdLine_c_or_C_Option)
return;
if (isCmdLine_c_or_C_Option)
@@ -13669,6 +13692,7 @@
int nFiles = 0;
int nX, nY, nZ, ptX, ptY;
int ptSigma = 0;
+ int ptCutoff = 0;
BitSet bs;
Vector v;
Point3f[] pts;
@@ -13883,6 +13907,8 @@
propertyValue = new Float(floatParameter(i));
if (colorRangeStage > 0)
++colorRangeStage;
+ else
+ ptCutoff = i;
break;
case Token.ionic:
case Token.vanderwaals:
@@ -14392,6 +14418,11 @@
propertyValue = data;
break;
case Token.string:
+ if (!surfaceObjectSeen && !planeSeen
+ && viewer.getParameter("_fileType").equals("Pdb") && ptSigma == 0
+ && ptCutoff == 0) {
+ addShapeProperty(propertyList, "sigma", new Float(1));
+ }
propertyName = surfaceObjectSeen || planeSeen ? "mapColor" : "readFile";
/*
* a file name, optionally followed by an integer file index. OR empty.
@@ -14534,6 +14565,8 @@
new Object[] { colorScheme,
isColorSchemeTranslucent ? Boolean.TRUE : Boolean.FALSE });
+ // TODO: addShapeProperty(propertyList, "variables", thisCommandVariables);
+
// OK, now send them all
setShapeProperty(iShape, "setProperties", propertyList);
@@ -14571,8 +14604,7 @@
float cutoff = ((Float) getShapeProperty(iShape, "cutoff"))
.floatValue();
if (Float.isNaN(cutoff) && ptSigma > 0) {
- iToken = ptSigma;
- error(ERROR_invalidArgument);
+ Logger.error("sigma not supported");
}
s += " created with cutoff=" + cutoff;
float[] minMax = (float[]) getShapeProperty(iShape, "minMaxInfo");
Modified: trunk/Jmol/src/org/jmol/script/ScriptFunction.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptFunction.java 2010-04-19 13:09:07 UTC (rev 12895)
+++ trunk/Jmol/src/org/jmol/script/ScriptFunction.java 2010-04-20 12:25:20 UTC (rev 12896)
@@ -119,7 +119,7 @@
for (int i = 0; i < nCommands; i++) {
function.lineNumbers[i] = (short) (lineNumbers[cmdpt0 + i] - line0);
function.lineIndices[i] = new int[] {lineIndices[cmdpt0 + i][0] - chpt0, lineIndices[cmdpt0 + i][1] - chpt0 };
- System.out.println("Line " + i + ": " + function.script.substring(function.lineIndices[i][0], function.lineIndices[i][1]));
+ //System.out.println("Line " + i + ": " + function.script.substring(function.lineIndices[i][0], function.lineIndices[i][1]));
aatoken[i] = (Token[]) lltoken.get(cmdpt0 + i);
if (aatoken[i].length > 0) {
Token tokenCommand = aatoken[i][0];
Modified: trunk/Jmol/src/org/jmol/shape/MeshCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/shape/MeshCollection.java 2010-04-19 13:09:07 UTC (rev 12895)
+++ trunk/Jmol/src/org/jmol/shape/MeshCollection.java 2010-04-20 12:25:20 UTC (rev 12896)
@@ -26,6 +26,7 @@
import org.jmol.g3d.*;
import org.jmol.viewer.JmolConstants;
+import org.jmol.viewer.StateManager;
import org.jmol.script.Token;
import java.util.BitSet;
@@ -58,7 +59,7 @@
protected int modelIndex;
protected boolean allowContourLines;
protected boolean haveContours = false;
-
+
public String[] title;
protected boolean allowMesh = true;
@@ -145,6 +146,11 @@
return;
}
+ if ("variables" == propertyName) {
+ if (currentMesh != null && currentMesh.scriptCommand != null && !currentMesh.scriptCommand.startsWith("{"))
+ currentMesh.scriptCommand = "{\n" + StateManager.getVariableList((Hashtable) value, 0, false) + "\n" + currentMesh.scriptCommand;
+ return;
+ }
if ("commandOption" == propertyName) {
String s = "# " + (String) value;
if (script.indexOf(s) < 0)
@@ -599,6 +605,9 @@
cmd = encapsulateData(cmd, mesh.data2, "2");
if (mesh.modelIndex >= 0 && modelCount > 1)
appendCmd(sb, "frame " + viewer.getModelNumberDotted(mesh.modelIndex));
+
+ if (cmd.charAt(0) == '{' && !cmd.endsWith("}"))
+ cmd += "\n}\n";
appendCmd(sb, cmd);
if (mesh.ptOffset != null)
appendCmd(sb, myType + " ID " + Escape.escape(mesh.thisID) + " offset " + Escape.escape(mesh.ptOffset));
Added: trunk/Jmol/src/org/jmol/util/SurfaceFileTyper.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/SurfaceFileTyper.java (rev 0)
+++ trunk/Jmol/src/org/jmol/util/SurfaceFileTyper.java 2010-04-20 12:25:20 UTC (rev 12896)
@@ -0,0 +1,154 @@
+/* $RCSfile$
+ * $Author: hansonr $
+ * $Date: 2007-04-05 09:07:28 -0500 (Thu, 05 Apr 2007) $
+ * $Revision: 7326 $
+ *
+ * Copyright (C) 2003-2005 The Jmol Development Team
+ *
+ * Contact: jmo...@li...
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public
+ * License as published by the Free Software Foundation; either
+ * version 2.1 of the License, or (at your option) any later version.
+ *
+ * This library is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this library; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.jmol.util;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedReader;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+
+public class SurfaceFileTyper {
+
+ /* moved to util because drag-drop can then determine an isosurface file
+ * type and automatically load the file
+ */
+
+ public final static String PMESH_BINARY_MAGIC_NUMBER = "PM" + '\1' + '\0';
+
+ public static String determineSurfaceFileType(InputStream is) {
+ BufferedReader br = new BufferedReader(new InputStreamReader(
+ new BufferedInputStream((InputStream) is, 8192)));
+ return SurfaceFileTyper.determineSurfaceFileType(br);
+ }
+
+ public static String determineSurfaceFileType(BufferedReader bufferedReader) {
+ // JVXL should be on the FIRST line of the file, but it may be
+ // after comments or missing.
+
+ // Apbs, Jvxl, or Cube, also efvet
+
+ String line;
+ LimitedLineReader br = new LimitedLineReader(bufferedReader, 16000);
+ //sure bets, but not REQUIRED:
+ if ((line = br.info()).length() == 0)
+ return null;
+ if (line.indexOf("<jvxl") >= 0 && line.indexOf("<?xml") >= 0)
+ return "JvxlXML";
+ if (line.indexOf("#JVXL+") >= 0)
+ return "Jvxl+";
+ if (line.indexOf("#JVXL") >= 0)
+ return "Jvxl";
+ if (line.indexOf("&plot") == 0)
+ return "Jaguar";
+ if (line.indexOf("MAP ") == 208)
+ return "MRC" + (line.charAt(67) == '\0' ? "L" : "B");
+ if (line.indexOf("<efvet ") >= 0)
+ return "Efvet";
+ if (line.indexOf(PMESH_BINARY_MAGIC_NUMBER) == 0)
+ return "Pmesh";
+ if ("\n\r".indexOf(line.charAt(0)) >= 0 && line.indexOf("ZYX") >= 0)
+ return "Xplor";
+ if (line.length() > 37 && line.charAt(36) == 0 && line.charAt(37) == 100)
+ return "DSN6B";
+ if (line.length() > 37 && line.charAt(37) == 100 && line.charAt(36) == 0)
+ return "DSN6L";
+
+ // Apbs, Jvxl, or Cube, maybe formatted Plt
+
+ line = br.readNonCommentLine();
+ if (line.indexOf("object 1 class gridpositions counts") == 0)
+ return "Apbs";
+
+ String[] tokens = Parser.getTokens(line);
+ line = br.readNonCommentLine();// second line
+ if (tokens.length == 2
+ && Parser.parseInt(tokens[0]) == 3
+ && Parser.parseInt(tokens[1])!= Integer.MIN_VALUE) {
+ tokens = Parser.getTokens(line);
+ if (tokens.length == 3
+ && Parser.parseInt(tokens[0])!= Integer.MIN_VALUE
+ && Parser.parseInt(tokens[1])!= Integer.MIN_VALUE
+ && Parser.parseInt(tokens[2])!= Integer.MIN_VALUE)
+ return "PltFormatted";
+ }
+ line = br.readNonCommentLine(); // third line
+ //next line should be the atom line
+ int nAtoms = Parser.parseInt(line);
+ if (nAtoms == Integer.MIN_VALUE)
+ return (line.indexOf("+") == 0 ? "Jvxl+" : null);
+ if (nAtoms >= 0)
+ return "Cube"; //Can't be a Jvxl file
+ nAtoms = -nAtoms;
+ for (int i = 4 + nAtoms; --i >=0;)
+ if ((line = br.readNonCommentLine()) == null)
+ return null;
+ int nSurfaces = Parser.parseInt(line);
+ if (nSurfaces == Integer.MIN_VALUE)
+ return null;
+ return (nSurfaces < 0 ? "Jvxl" : "Cube"); //Final test looks at surface definition line
+ }
+
+}
+
+class LimitedLineReader {
+ //from Resolver
+ private char[] buf;
+ private int cchBuf;
+ private int ichCurrent;
+
+ LimitedLineReader(BufferedReader bufferedReader, int readLimit) {
+ buf = new char[readLimit];
+ try {
+ bufferedReader.mark(readLimit);
+ cchBuf = bufferedReader.read(buf);
+ ichCurrent = 0;
+ bufferedReader.reset();
+ } catch (Exception e) {
+ }
+ }
+
+ protected String info() {
+ return new String(buf);
+ }
+
+ protected String readNonCommentLine() {
+ while (ichCurrent < cchBuf) {
+ int ichBeginningOfLine = ichCurrent;
+ char ch = 0;
+ while (ichCurrent < cchBuf &&
+ (ch = buf[ichCurrent++]) != '\r' && ch != '\n') {
+ }
+ int cchLine = ichCurrent - ichBeginningOfLine;
+ if (ch == '\r' && ichCurrent < cchBuf && buf[ichCurrent] == '\n')
+ ++ichCurrent;
+ if (buf[ichBeginningOfLine] == '#') // flush comment lines;
+ continue;
+ StringBuffer sb = new StringBuffer(cchLine);
+ sb.append(buf, ichBeginningOfLine, cchLine);
+ return sb.toString();
+ }
+ return "";
+ }
+}
+
Property changes on: trunk/Jmol/src/org/jmol/util/SurfaceFileTyper.java
___________________________________________________________________
Added: svn:mime-type
+ text/plain
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-04-19 13:09:07 UTC (rev 12895)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2010-04-20 12:25:20 UTC (rev 12896)
@@ -3,6 +3,8 @@
version=12.0.RC7_dev
+# new feature: drag-and-drop defaults for map files and PDB files
+# bug fix: VRML exporter fails to remove duplicate spheres if not same color
# bug fix: states not saving correct path to isosurface files
# new feature: spacefill, halos, stars -x.y is "ONLY" as for other shapes
# bug fix: _atomPicked not updated for centering or other non-identify actions
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-04-19 13:09:07 UTC (rev 12895)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2010-04-20 12:25:20 UTC (rev 12896)
@@ -55,6 +55,7 @@
import org.jmol.util.Escape;
import org.jmol.util.JpegEncoder;
import org.jmol.util.OutputStringBuffer;
+import org.jmol.util.SurfaceFileTyper;
import org.jmol.util.Logger;
import org.jmol.util.Measure;
@@ -1717,28 +1718,42 @@
private final static int FILE_STATUS_MODELSET_CREATED = 3;
private final static int FILE_STATUS_MODELS_DELETED = 5;
+ /**
+ * opens a file as a model, a script, or a surface via the creation of a
+ * script that is queued \t at the beginning disallows script option
+ *
+ * @param fileName
+ */
public void openFileAsynchronously(String fileName) {
- // not really asynchronously -- put on the queue just like any other file
- // Jmol app file dropper, main, OpenUrlAction, RecentFilesAction
- if (fileName.indexOf(".jvxl") >= 0 || fileName.indexOf(".xjvxl") >= 0) {
- evalString("isosurface " + Escape.escape(fileName));
- return;
- }
boolean allowScript = (!fileName.startsWith("\t"));
if (!allowScript)
fileName = fileName.substring(1);
fileName = fileName.replace('\\', '/');
if (isApplet && fileName.indexOf("://") < 0)
fileName = "file://" + (fileName.startsWith("/") ? "" : "/") + fileName;
- String type = fileManager.getFileTypeName(fileName);
- // checkHalt("exit", true);
- // assumes a Jmol script file if no other file type
- allowScript &= (type == null);
- if (scriptEditorVisible && allowScript)
+
+ String cmd = null;
+ if (fileName.endsWith("jvxl"))
+ cmd = "isosurface ";
+ else if (!fileName.endsWith(".spt")) {
+ String type = fileManager.getFileTypeName(fileName);
+ if (type == null) {
+ type = SurfaceFileTyper
+ .determineSurfaceFileType(getBufferedInputStream(fileName));
+ if (type != null) {
+ evalString("if (_filetype == 'Pdb') { isosurface sigma 1.0 within 2.0 {*} " + Escape.escape(fileName) + " mesh nofill }; else; { isosurface " + Escape.escape(fileName) + "}");
+ return;
+ }
+ } else if (!type.equals("spt")) {
+ evalString("zap; load " + Escape.escape(fileName)
+ + ";if (_loadScript = '' && defaultLoadScript == '' && _filetype == 'Pdb') { select protein or nucleic;cartoons Only;color structure; select * }" );
+ return;
+ }
+ }
+ if (allowScript && scriptEditorVisible && cmd == null)
showEditor(new String[] { fileName, getFileAsString(fileName) });
else
- evalString((allowScript ? "script " : "zap;load ")
- + Escape.escape(fileName));
+ evalString((cmd == null ? "script " : cmd) + Escape.escape(fileName));
}
/**
Modified: trunk/Jmol/src/org/openscience/jmol/app/JmolApp.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/JmolApp.java 2010-04-19 13:09:07 UTC (rev 12895)
+++ trunk/Jmol/src/org/openscience/jmol/app/JmolApp.java 2010-04-20 12:25:20 UTC (rev 12896)
@@ -453,7 +453,7 @@
// Open a file if one is given as an argument -- note, this CAN be a
// script file
if (modelFilename != null) {
- viewer.openFileAsynchronously(modelFilename);
+ viewer.openFile(modelFilename);
}
// OK, by now it is time to execute the script
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