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[Jmol-commits] SF.net SVN: jmol:[11776] trunk/Jmol/src/org/jmol
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From: <ha...@us...> - 2009-11-22 19:16:44
|
Revision: 11776
http://jmol.svn.sourceforge.net/jmol/?rev=11776&view=rev
Author: hansonr
Date: 2009-11-22 19:16:27 +0000 (Sun, 22 Nov 2009)
Log Message:
-----------
version=11.9.10_dev # bug fix: occasional null pointer error during ZAP due to continued rendering by
# previous graphic painting thread
# code: refactoring of FileManager and clean-up of Viewer code
# in relation to model loading.
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/api/JmolViewer.java
trunk/Jmol/src/org/jmol/applet/Jmol.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/viewer/ActionManager.java
trunk/Jmol/src/org/jmol/viewer/FileManager.java
trunk/Jmol/src/org/jmol/viewer/Jmol.properties
trunk/Jmol/src/org/jmol/viewer/MouseManager.java
trunk/Jmol/src/org/jmol/viewer/RepaintManager.java
trunk/Jmol/src/org/jmol/viewer/Viewer.java
Modified: trunk/Jmol/src/org/jmol/api/JmolViewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/api/JmolViewer.java 2009-11-22 19:15:53 UTC (rev 11775)
+++ trunk/Jmol/src/org/jmol/api/JmolViewer.java 2009-11-22 19:16:27 UTC (rev 11776)
@@ -361,7 +361,7 @@
abstract public boolean showModelSetDownload();
- abstract public void repaintView();
+ abstract public void notifyViewerRepaintDone();
abstract public boolean getBooleanProperty(String propertyName);
abstract public boolean getBooleanProperty(String key, boolean doICare);
Modified: trunk/Jmol/src/org/jmol/applet/Jmol.java
===================================================================
--- trunk/Jmol/src/org/jmol/applet/Jmol.java 2009-11-22 19:15:53 UTC (rev 11775)
+++ trunk/Jmol/src/org/jmol/applet/Jmol.java 2009-11-22 19:16:27 UTC (rev 11776)
@@ -494,7 +494,7 @@
if (REQUIRE_PROGRESSBAR && !isSigned && !hasProgressBar
&& paintCounter < 30 && (paintCounter & 1) == 0) {
printProgressbarMessage(g);
- viewer.repaintView();
+ viewer.notifyViewerRepaintDone();
} else {
//System.out.println("UPDATE1: " + source + " " + Thread.currentThread());
//System.out.println(fullName + " update gRight = " + gRight);
@@ -513,7 +513,8 @@
private final static String[] progressbarMsgs = {
"Jmol developer alert!",
"",
- "Please use jmol.js. You are missing the require 'progressbar' parameter.",
+ "Please use jmol.js. You are missing the ",
+ "required 'progressbar' parameter.",
" <param name='progressbar' value='true' />", };
private void printProgressbarMessage(Graphics g) {
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2009-11-22 19:15:53 UTC (rev 11775)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2009-11-22 19:16:27 UTC (rev 11776)
@@ -24,6 +24,8 @@
package org.jmol.script;
import java.awt.Image;
+import java.io.BufferedReader;
+import java.io.StringReader;
import java.util.BitSet;
import java.util.Enumeration;
import java.util.Hashtable;
@@ -6516,8 +6518,9 @@
String modelName = null;
String filename = null;
String[] filenames = null;
+ String[] tempFileInfo = null;
int tokType = 0;
- boolean doLoadFiles = (!isSyntaxCheck || isCmdLine_C_Option);
+ boolean doLoadFiles = (!isSyntaxCheck || isCmdLine_C_Option);
String errMsg = null;
String sOptions = "";
if (statementLength == 1) {
@@ -6535,14 +6538,15 @@
i = 2;
loadScript.append(" " + modelName);
isAppend = (modelName.equalsIgnoreCase("append"));
- boolean atomDataOnly = Parser.isOneOf(modelName.toLowerCase(),
- JmolConstants.LOAD_ATOM_DATA_TYPES);
- if (atomDataOnly) {
+ tokType = (Parser.isOneOf(modelName.toLowerCase(),
+ JmolConstants.LOAD_ATOM_DATA_TYPES) ? Token
+ .getTokenFromName(modelName.toLowerCase()).tok : 0);
+ if (tokType > 0) {
htParams.put("atomDataOnly", Boolean.TRUE);
htParams.put("modelNumber", new Integer(1));
- tokType = Token.getTokenFromName(modelName.toLowerCase()).tok;
if (tokType == Token.vibration)
tokType = Token.vibXyz;
+ tempFileInfo = viewer.getFileInfo();
}
if (isAppend
&& ((filename = optParameterAsString(2))
@@ -6552,7 +6556,7 @@
loadScript.append(" " + modelName);
i++;
}
- if (atomDataOnly)
+ if (tokType > 0)
isAppend = true;
if (modelName.equalsIgnoreCase("trajectory")
|| modelName.equalsIgnoreCase("models")) {
@@ -6752,15 +6756,29 @@
if (!doLoadFiles)
return;
if (filenames == null) {
- //standard file loading here
+ // standard file loading here
if (filename.startsWith("@") && filename.length() > 1) {
htParams.put("fileData", getStringParameter(filename.substring(1),
false));
filename = "string";
}
}
- errMsg = viewer.loadModelFromFile(filename, filenames, isAppend, htParams, tokType);
+
+ // OK, we are ready to load the data and create the model set
+
+ errMsg = viewer.loadModelFromFile(filename, filenames, isAppend, htParams,
+ tokType);
+
+ if (tokType > 0) {
+ // we are just loading an atom property
+ // reset the file info in FileManager, check for errors, and return
+ viewer.setFileInfo(tempFileInfo);
+ if (errMsg != null && !isCmdLine_c_or_C_Option)
+ evalError(errMsg, null);
+ return;
+ }
if (filenames == null) {
+ // a single file or string -- complete the loadScript
loadScript.append(" ");
if (!filename.equals("string") && !filename.equals("string[]"))
loadScript.append("/*file*/");
@@ -6768,18 +6786,16 @@
.get("fullPathName")));
loadScript.append(sOptions);
}
- if (tokType == 0)
- viewer.addLoadScript(loadScript.toString());
+ viewer.addLoadScript(loadScript.toString());
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");
+ errMsg = TextFormat.trim(errMsg, "\n");
runScript("script \"" + errMsg.substring(40) + "\"");
return;
}
evalError(errMsg, null);
}
-
if (isAppend && (appendNew || nFiles > 1)) {
viewer.setAnimationRange(-1, -1);
viewer.setCurrentModelIndex(modelCount);
@@ -6799,7 +6815,7 @@
}
if (msg.length() > 0)
Logger.info(msg);
- if (defaultScript.length() > 0 && !isCmdLine_c_or_C_Option)
+ if (defaultScript.length() > 0 && !isCmdLine_c_or_C_Option)
// NOT checking embedded scripts in some cases
runScript(defaultScript);
}
@@ -12863,7 +12879,7 @@
sdata = TextFormat.replaceAllCharacters(sdata, "{,}|", ' ');
if (logMessages)
Logger.debug("pmesh inline data:\n" + sdata);
- t = (isSyntaxCheck ? null : viewer.getBufferedReaderForString(sdata));
+ t = (isSyntaxCheck ? null : new BufferedReader(new StringReader(sdata)));
} else {
if (thisCommand.indexOf("# FILE" + nFiles + "=") >= 0)
filename = extractCommandOption("# FILE" + nFiles);
Modified: trunk/Jmol/src/org/jmol/viewer/ActionManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2009-11-22 19:15:53 UTC (rev 11775)
+++ trunk/Jmol/src/org/jmol/viewer/ActionManager.java 2009-11-22 19:16:27 UTC (rev 11776)
@@ -237,8 +237,10 @@
Binding dragBinding;
Binding rasmolBinding;
+ ActionManager aman;
ActionManager(Viewer viewer) {
this.viewer = viewer;
+ aman = this;
binding = jmolBinding = new JmolBinding();
}
@@ -940,8 +942,7 @@
Thread.currentThread().setPriority(Thread.MIN_PRIORITY);
int hoverDelay;
try {
- while (hoverWatcherThread != null
- && (hoverDelay = viewer.getHoverDelay()) > 0) {
+ while (Thread.currentThread().equals(hoverWatcherThread) && (hoverDelay = viewer.getHoverDelay()) > 0) {
Thread.sleep(hoverDelay);
if (xCurrent == mouseMovedX && yCurrent == mouseMovedY
&& timeCurrent == mouseMovedTime) { // the last event was mouse
@@ -949,12 +950,13 @@
long currentTime = System.currentTimeMillis();
int howLong = (int) (currentTime - mouseMovedTime);
if (howLong > hoverDelay) {
- if (hoverWatcherThread != null && !viewer.getInMotion()
+ if (Thread.currentThread().equals(hoverWatcherThread) && !viewer.getInMotion()
&& !viewer.getSpinOn() && !viewer.getNavOn()
&& !viewer.checkObjectHovered(xCurrent, yCurrent)) {
int atomIndex = viewer.findNearestAtomIndex(xCurrent, yCurrent);
- if (atomIndex >= 0)
+ if (atomIndex >= 0) {
hoverOn(atomIndex);
+ }
}
}
}
@@ -964,7 +966,6 @@
} catch (Exception ie) {
Logger.debug("Hover Exception: " + ie);
}
- hoverWatcherThread = null;
}
}
Modified: trunk/Jmol/src/org/jmol/viewer/FileManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/FileManager.java 2009-11-22 19:15:53 UTC (rev 11775)
+++ trunk/Jmol/src/org/jmol/viewer/FileManager.java 2009-11-22 19:16:27 UTC (rev 11776)
@@ -61,44 +61,99 @@
import java.util.Hashtable;
import java.util.Vector;
-/* ***************************************************************
- * will not work with applet
- import java.net.URI;
- import java.net.URISyntaxException;
- import java.util.Enumeration;
- import org.openscience.jmol.io.ChemFileReader;
- import org.openscience.jmol.io.ReaderFactory;
- */
-
public class FileManager {
protected Viewer viewer;
- // for applet proxy
- private URL appletDocumentBase = null;
- private URL appletCodeBase = null; //unused currently
- private String appletProxy;
+ FileManager(Viewer viewer) {
+ this.viewer = viewer;
+ clear();
+ }
- // for expanding names into full path names
- //private boolean isURL;
+ void clear() {
+ setLoadScript("", false);
+ fullPathName = fileName = nameAsGiven = "zapped";
+ }
+
+ private String loadScript;
+
+ String getLoadScript() {
+ return loadScript;
+ }
+
+ private void setLoadScript(String script, boolean isAppend) {
+ if (loadScript == null || !isAppend)
+ loadScript = "";
+ loadScript += viewer.getLoadState();
+ addLoadScript(script);
+ }
+
+ void addLoadScript(String script) {
+ if (script == null)
+ return;
+ if (script.equals("-")) {
+ loadScript = "";
+ return;
+ }
+ loadScript += " " + script + ";\n";
+ }
+
private String nameAsGiven = "zapped";
private String fullPathName;
private String fileName;
- private String fileType;
-
private String inlineData;
+ //TODO: We might consider an option to not preserve inlineData in certain cases where
+ // data are huge. The reason to save the data is that we can then use load ""
+ //
+ void setFileInfo(String[] fileInfo) {
+ // used by ScriptEvaluator dataFrame and load methods to temporarily save the state here
+ fullPathName = fileInfo[0];
+ fileName = fileInfo[1];
+ nameAsGiven = fileInfo[2];
+ inlineData = fileInfo[3];
+ loadScript = fileInfo[4];
+ }
+
+ String[] getFileInfo() {
+ // used by ScriptEvaluator dataFrame method
+ return new String[] { fullPathName, fileName, nameAsGiven, inlineData, loadScript };
+ }
+
+ String getFullPathName() {
+ return fullPathName != null ? fullPathName : nameAsGiven;
+ }
+
+ String getFileName() {
+ return fileName != null ? fileName : nameAsGiven;
+ }
+
String getInlineData(int iData) {
return (iData < 0 ? inlineData : "");
}
- private String loadScript;
+ // for applet proxy
+ private URL appletDocumentBase = null;
+ private URL appletCodeBase = null; //unused currently
+ private String appletProxy;
- FileManager(Viewer viewer) {
- this.viewer = viewer;
- clear();
+ String getAppletDocumentBase() {
+ return (appletDocumentBase == null ? "" : appletDocumentBase.toString());
}
+ void setAppletContext(URL documentBase, URL codeBase, String jmolAppletProxy) {
+ appletDocumentBase = documentBase;
+ appletCodeBase = codeBase;
+ appletProxy = jmolAppletProxy;
+ Logger.info("appletDocumentBase=" + appletDocumentBase
+ + "\nappletCodeBase=" + appletCodeBase);
+ }
+
+ void setAppletProxy(String appletProxy) {
+ this.appletProxy = (appletProxy == null || appletProxy.length() == 0 ? null
+ : appletProxy);
+ }
+
String getState(StringBuffer sfunc) {
StringBuffer commands = new StringBuffer();
if (sfunc != null) {
@@ -134,35 +189,22 @@
return null;
}
- void clear() {
- setLoadScript("", false);
- fullPathName = fileName = nameAsGiven = "zapped";
+ private static BufferedReader getBufferedReaderForString(String string) {
+ return new BufferedReader(new StringReader(string));
}
- String getLoadScript() {
- return loadScript;
+ private String getZipDirectoryAsString(String fileName) {
+ return ZipUtil
+ .getZipDirectoryAsStringAndClose((InputStream) getInputStreamOrErrorMessageFromName(
+ fileName, false));
}
- private void setLoadScript(String script, boolean isAppend) {
- if (loadScript == null || !isAppend)
- loadScript = "";
- loadScript += viewer.getLoadState();
- addLoadScript(script);
- }
-
- void addLoadScript(String script) {
- if (script == null)
- return;
- if (script.equals("-")) {
- loadScript = "";
- return;
- }
- loadScript += " " + script + ";\n";
- }
-
+ /////////////// createAtomSetCollectionFromXXX methods /////////////////
+ // where XXX = File, Files, String, Strings, ArrayData, DOM, Reader
+
/*
- * note -- getAtomSetCollectionFromXXX methods
+ * note -- createAtomSetCollectionFromXXX methods
* were "openXXX" before refactoring 11/29/2008 -- BH
*
* The problem was that while they did open the file, they
@@ -188,7 +230,7 @@
setLoadScript(loadScript, isAppend);
int pt = name.indexOf("::");
nameAsGiven = (pt >= 0 ? name.substring(pt + 2) : name);
- fileType = (pt >= 0 ? name.substring(0, pt) : null);
+ String fileType = (pt >= 0 ? name.substring(0, pt) : null);
Logger.info("\nFileManager.getAtomSetCollectionFromFile(" + nameAsGiven
+ ")" + (name.equals(nameAsGiven) ? "" : " //" + name));
fullPathName = null;
@@ -218,7 +260,7 @@
for (int i = 0; i < fileNames.length; i++) {
int pt = fileNames[i].indexOf("::");
nameAsGiven = (pt >= 0 ? fileNames[i].substring(pt + 2) : fileNames[i]);
- fileType = (pt >= 0 ? fileNames[i].substring(0, pt) : null);
+ String fileType = (pt >= 0 ? fileNames[i].substring(0, pt) : null);
String[] names = classifyName(nameAsGiven, true);
if (names.length == 1)
return names[0];
@@ -326,138 +368,162 @@
Reader reader, Hashtable htParams) {
this.fullPathName = fullPathName;
fileName = name;
- fileType = null;
FileReader fileReader = new FileReader(fullPathName, fullPathName,
- fileType, new BufferedReader(reader), htParams);
+ null, new BufferedReader(reader), htParams);
fileReader.run();
return fileReader.atomSetCollection;
}
- public Object getFileAsBytes(String name) {
- //?? used by eval of "WRITE FILE"
- // will be full path name
- if (name == null)
- return null;
- String[] subFileList = null;
- if (name.indexOf("|") >= 0)
- name = (subFileList = TextFormat.split(name, "|"))[0];
- Object t = getInputStreamOrErrorMessageFromName(name, false);
- if (t instanceof String)
- return "Error:" + t;
- try {
- BufferedInputStream bis = new BufferedInputStream((InputStream) t, 8192);
- InputStream is = bis;
- Object bytes = (ZipUtil.isZipFile(is) && subFileList != null
- && 1 < subFileList.length ? ZipUtil.getZipFileContentsAsBytes(is,
- subFileList, 1) : ZipUtil.getStreamAsBytes(bis));
- is.close();
- return bytes;
- } catch (Exception ioe) {
- return ioe.getMessage();
- }
+ /////////////// generally useful file I/O methods /////////////////
+
+ // mostly internal to FileManager and its enclosed classes
+
+ BufferedInputStream getBufferedInputStream(String fullPathName) {
+ Object ret = getBufferedReaderOrErrorMessageFromName(fullPathName,
+ new String[2], true, true);
+ return (ret instanceof BufferedInputStream ? (BufferedInputStream) ret
+ : null);
}
- /**
- *
- * @param data
- * [0] initially path name, but returned as full path name; [1]file
- * contents (directory listing for a ZIP/JAR file) or error string
- * @param nBytesMax
- * @param doSpecialLoad
- * @return true if successful; false on error
- */
-
- boolean getFileDataOrErrorAsString(String[] data, int nBytesMax, boolean doSpecialLoad) {
- data[1] = "";
- String name = data[0];
- if (name == null)
- return false;
- Object t = getBufferedReaderOrErrorMessageFromName(name, data, false, doSpecialLoad);
- if (t instanceof String) {
- data[1] = (String) t;
- return false;
- }
+ Object getInputStreamOrErrorMessageFromName(String name, boolean showMsg) {
+ String errorMessage = null;
+ int iurlPrefix;
+ for (iurlPrefix = urlPrefixes.length; --iurlPrefix >= 0;)
+ if (name.startsWith(urlPrefixes[iurlPrefix]))
+ break;
+ boolean isURL = (iurlPrefix >= 0);
+ boolean isApplet = (appletDocumentBase != null);
+ InputStream in = null;
+ //int length;
try {
- BufferedReader br = (BufferedReader) t;
- StringBuffer sb = new StringBuffer(8192);
- String line;
- if (nBytesMax == Integer.MAX_VALUE) {
- while ((line = br.readLine()) != null)
- sb.append(line).append('\n');
+ if (isApplet || isURL) {
+ if (isApplet && isURL && appletProxy != null)
+ name = appletProxy + "?url=" + URLEncoder.encode(name, "utf-8");
+ URL url = (isApplet ? new URL(appletDocumentBase, name) : new URL(name));
+ name = url.toString();
+ if (showMsg)
+ Logger.info("FileManager opening " + url.toString());
+ URLConnection conn = url.openConnection();
+ //length = conn.getContentLength();
+ in = conn.getInputStream();
} else {
- int n = 0;
- int len;
- while (n < nBytesMax && (line = br.readLine()) != null) {
- if (nBytesMax - n < (len = line.length()) + 1)
- line = line.substring(0, nBytesMax - n - 1);
- sb.append(line).append('\n');
- n += len + 1;
- }
+ if (showMsg)
+ Logger.info("FileManager opening " + name);
+ File file = new File(name);
+ //length = (int) file.length();
+ in = new FileInputStream(file);
}
- br.close();
- data[1] = sb.toString();
- return true;
- } catch (Exception ioe) {
- data[1] = ioe.getMessage();
- return false;
+ return in;
+ } catch (Exception e) {
+ try {
+ if (in != null)
+ in.close();
+ } catch (IOException e1) {
+ }
+ errorMessage = "" + e;
}
+ return errorMessage;
}
- Object getFileAsImage(String name, Hashtable htParams) {
- if (name == null)
- return "";
+ Object getBufferedReaderOrErrorMessageFromName(String name,
+ String[] fullPathNameReturn,
+ boolean isBinary, boolean doSpecialLoad) {
String[] names = classifyName(name, true);
if (names == null)
return "cannot read file name: " + name;
- Image image = null;
- //try {
- fullPathName = names[0].replace('\\', '/');
- if (urlTypeIndex(fullPathName) >= 0)
- try {
- image = Toolkit.getDefaultToolkit().createImage(new URL(fullPathName));
- } catch (Exception e) {
- return "bad URL: " + fullPathName;
+ if (fullPathNameReturn != null)
+ fullPathNameReturn[0] = names[0].replace('\\', '/');
+ return getUnzippedBufferedReaderOrErrorMessageFromName(names[0], false,
+ isBinary, false, doSpecialLoad);
+ }
+
+ Object getUnzippedBufferedReaderOrErrorMessageFromName(
+ String name,
+ boolean allowZipStream,
+ boolean asInputStream,
+ boolean isTypeCheckOnly,
+ boolean doSpecialLoad) {
+ String[] subFileList = null;
+ String[] info = (doSpecialLoad ? viewer.getModelAdapter().specialLoad(name,
+ "filesNeeded?") : null);
+ if (info != null) {
+ if (isTypeCheckOnly)
+ return info;
+ if (info[2] != null) {
+ String header = info[1];
+ Hashtable fileData = new Hashtable();
+ if (info.length == 3) {
+ // we need information from the output file, info[2]
+ String name0 = getObjectAsSections(info[2], header, fileData);
+ fileData.put("OUTPUT", name0);
+ info = viewer.getModelAdapter().specialLoad(name,
+ (String) fileData.get(name0));
+ if (info.length == 3) {
+ // might have a second option
+ name0 = getObjectAsSections(info[2], header, fileData);
+ fileData.put("OUTPUT", name0);
+ info = viewer.getModelAdapter().specialLoad(info[1],
+ (String) fileData.get(name0));
+ }
+ }
+ // load each file individually, but return files IN ORDER
+ StringBuffer sb = new StringBuffer();
+ sb.append(fileData.get(fileData.get("OUTPUT")));
+ for (int i = 2; i < info.length; i++) {
+ name = info[i];
+ name = getObjectAsSections(name, header, fileData);
+ Logger.info("reading " + name);
+ String s = (String) fileData.get(name);
+ sb.append(s);
+ }
+ return getBufferedReaderForString(sb.toString());
}
- else
- image = Toolkit.getDefaultToolkit().createImage(fullPathName);
+ // continuing...
+ // here, for example, for an SPT file load that is not just a type check
+ // (type check is only for application file opening and drag-drop to
+ // determine if
+ // script or load command should be used)
+ }
+ if (name.indexOf("|") >= 0)
+ name = (subFileList = TextFormat.split(name, "|"))[0];
+ Object t = getInputStreamOrErrorMessageFromName(name, true);
+ if (t instanceof String)
+ return t;
try {
- MediaTracker mediaTracker = new MediaTracker(viewer.getDisplay());
- mediaTracker.addImage(image, 0);
- mediaTracker.waitForID(0);
- /* SUN but here for malformed URL - can't trap
- Uncaught error fetching image:
- java.lang.NullPointerException
- at sun.net.www.ParseUtil.toURI(Unknown Source)
- at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
- at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source)
- at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
- at sun.awt.image.URLImageSource.getDecoder(Unknown Source)
- at sun.awt.image.InputStreamImageSource.doFetch(Unknown Source)
- at sun.awt.image.ImageFetcher.fetchloop(Unknown Source)
- at sun.awt.image.ImageFetcher.run(Unknown Source)
- */
- } catch (Exception e) {
- return e.getMessage() + " opening " + fullPathName;
+ BufferedInputStream bis = new BufferedInputStream((InputStream) t, 8192);
+ InputStream is = bis;
+ if (CompoundDocument.isCompoundDocument(is)) {
+ CompoundDocument doc = new CompoundDocument(bis);
+ return getBufferedReaderForString(doc.getAllData("Molecule").toString());
+ } else if (ZipUtil.isGzip(is)) {
+ do {
+ is = new BufferedInputStream(new GZIPInputStream(is));
+ } while (ZipUtil.isGzip(is));
+ } else if (ZipUtil.isZipFile(is)) {
+ if (allowZipStream)
+ return new ZipInputStream(bis);
+ if (asInputStream)
+ return (InputStream) ZipUtil.getZipFileContents(is, subFileList, 1,
+ true);
+ // danger -- converting bytes to String here.
+ // we lose 128-156 or so.
+ String s = (String) ZipUtil.getZipFileContents(is, subFileList, 1,
+ false);
+ is.close();
+ return getBufferedReaderForString(s);
+ }
+ if (asInputStream)
+ return is;
+ return new BufferedReader(new InputStreamReader(is));
+ } catch (Exception ioe) {
+ return ioe.getMessage();
}
- if (image.getWidth(null) < 1)
- return "invalid or missing image " + fullPathName;
- htParams.put("fullPathName", fullPathName);
- return image;
}
- private String getObjectAsSections(String[] info, Hashtable fileData) {
- // load each file individually, but return files IN ORDER
- String header = info[1];
- StringBuffer sb = new StringBuffer();
- sb.append(fileData.get(fileData.get("OUTPUT")));
- for (int i = 2; i < info.length; i++) {
- String name = info[i];
- name = getObjectAsSections(name, header, fileData);
- Logger.info("reading " + name);
- String s = (String) fileData.get(name);
- sb.append(s);
- }
- return sb.toString();
+ String[] getZipDirectory(String fileName, boolean addManifest) {
+ return ZipUtil.getZipDirectoryAndClose(
+ (InputStream) getInputStreamOrErrorMessageFromName(fileName, false),
+ addManifest);
}
/**
@@ -551,49 +617,118 @@
return name0;
}
- String getFullPathName() {
- return fullPathName != null ? fullPathName : nameAsGiven;
- }
-
- void setFileInfo(String[] fileInfo) {
+ Object getFileAsBytes(String name) {
+ //?? used by eval of "WRITE FILE"
+ // will be full path name
+ if (name == null)
+ return null;
+ String[] subFileList = null;
+ if (name.indexOf("|") >= 0)
+ name = (subFileList = TextFormat.split(name, "|"))[0];
+ Object t = getInputStreamOrErrorMessageFromName(name, false);
+ if (t instanceof String)
+ return "Error:" + t;
try {
- fullPathName = fileInfo[0];
- fileName = fileInfo[1];
- inlineData = fileInfo[2];
- loadScript = fileInfo[3];
- } catch (Exception e) {
- Logger.error("Exception saving file info: " + e.getMessage());
+ BufferedInputStream bis = new BufferedInputStream((InputStream) t, 8192);
+ InputStream is = bis;
+ Object bytes = (ZipUtil.isZipFile(is) && subFileList != null
+ && 1 < subFileList.length ? ZipUtil.getZipFileContentsAsBytes(is,
+ subFileList, 1) : ZipUtil.getStreamAsBytes(bis));
+ is.close();
+ return bytes;
+ } catch (Exception ioe) {
+ return ioe.getMessage();
}
}
- String[] getFileInfo() {
- return new String[] { fullPathName, fileName, inlineData, loadScript };
- }
+ /**
+ *
+ * @param data
+ * [0] initially path name, but returned as full path name; [1]file
+ * contents (directory listing for a ZIP/JAR file) or error string
+ * @param nBytesMax
+ * @param doSpecialLoad
+ * @return true if successful; false on error
+ */
- String getFileName() {
- return fileName != null ? fileName : nameAsGiven;
+ boolean getFileDataOrErrorAsString(String[] data, int nBytesMax, boolean doSpecialLoad) {
+ data[1] = "";
+ String name = data[0];
+ if (name == null)
+ return false;
+ Object t = getBufferedReaderOrErrorMessageFromName(name, data, false, doSpecialLoad);
+ if (t instanceof String) {
+ data[1] = (String) t;
+ return false;
+ }
+ try {
+ BufferedReader br = (BufferedReader) t;
+ StringBuffer sb = new StringBuffer(8192);
+ String line;
+ if (nBytesMax == Integer.MAX_VALUE) {
+ while ((line = br.readLine()) != null)
+ sb.append(line).append('\n');
+ } else {
+ int n = 0;
+ int len;
+ while (n < nBytesMax && (line = br.readLine()) != null) {
+ if (nBytesMax - n < (len = line.length()) + 1)
+ line = line.substring(0, nBytesMax - n - 1);
+ sb.append(line).append('\n');
+ n += len + 1;
+ }
+ }
+ br.close();
+ data[1] = sb.toString();
+ return true;
+ } catch (Exception ioe) {
+ data[1] = ioe.getMessage();
+ return false;
+ }
}
- String getAppletDocumentBase() {
- if (appletDocumentBase == null)
+ Object getFileAsImage(String name, Hashtable htParams) {
+ if (name == null)
return "";
- return appletDocumentBase.toString();
+ String[] names = classifyName(name, true);
+ if (names == null)
+ return "cannot read file name: " + name;
+ Image image = null;
+ //try {
+ fullPathName = names[0].replace('\\', '/');
+ if (urlTypeIndex(fullPathName) >= 0)
+ try {
+ image = Toolkit.getDefaultToolkit().createImage(new URL(fullPathName));
+ } catch (Exception e) {
+ return "bad URL: " + fullPathName;
+ }
+ else
+ image = Toolkit.getDefaultToolkit().createImage(fullPathName);
+ try {
+ MediaTracker mediaTracker = new MediaTracker(viewer.getDisplay());
+ mediaTracker.addImage(image, 0);
+ mediaTracker.waitForID(0);
+ /* SUN but here for malformed URL - can't trap
+ Uncaught error fetching image:
+ java.lang.NullPointerException
+ at sun.net.www.ParseUtil.toURI(Unknown Source)
+ at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
+ at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source)
+ at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
+ at sun.awt.image.URLImageSource.getDecoder(Unknown Source)
+ at sun.awt.image.InputStreamImageSource.doFetch(Unknown Source)
+ at sun.awt.image.ImageFetcher.fetchloop(Unknown Source)
+ at sun.awt.image.ImageFetcher.run(Unknown Source)
+ */
+ } catch (Exception e) {
+ return e.getMessage() + " opening " + fullPathName;
+ }
+ if (image.getWidth(null) < 1)
+ return "invalid or missing image " + fullPathName;
+ htParams.put("fullPathName", fullPathName);
+ return image;
}
- void setAppletContext(URL documentBase, URL codeBase, String jmolAppletProxy) {
- appletDocumentBase = documentBase;
- appletCodeBase = codeBase;
- Logger.info("appletDocumentBase=" + appletDocumentBase
- + "\nappletCodeBase=" + appletCodeBase);
- // dumpDocumentBase("" + documentBase);
- appletProxy = jmolAppletProxy;
- }
-
- void setAppletProxy(String appletProxy) {
- this.appletProxy = (appletProxy == null || appletProxy.length() == 0 ? null
- : appletProxy);
- }
-
private final static int URL_LOCAL = 3;
private final static String[] urlPrefixes = { "http:", "https:", "ftp:",
"file:" };
@@ -607,10 +742,6 @@
return -1;
}
- static String shortNameOf(String name) {
- name = TextFormat.trim(name.replace('\\', '/'), "/");
- return name.substring(name.lastIndexOf("/") + 1);
- }
/**
*
* @param name
@@ -675,6 +806,20 @@
return names;
}
+ private static String addDirectory(String defaultDirectory, String name) {
+ if (defaultDirectory.length() == 0)
+ return name;
+ char ch = (name.length() > 0 ? name.charAt(0) : ' ');
+ String s = defaultDirectory.toLowerCase();
+ if ((s.endsWith(".zip") || s.endsWith(".tar")) && ch != '|' && ch != '/')
+ defaultDirectory += "|";
+ return defaultDirectory
+ + (ch == '/'
+ || ch == '/'
+ || (ch = defaultDirectory.charAt(defaultDirectory.length() - 1)) == '|'
+ || ch == '/' ? "" : "/") + name;
+ }
+
String getDefaultDirectory(String name) {
String[] names = classifyName(name, true);
if (names == null)
@@ -683,7 +828,7 @@
return (names == null ? "" : name.substring(0, name.lastIndexOf("/")));
}
- public static String fixPath(String path) {
+ private static String fixPath(String path) {
path = path.replace('\\', '/');
path = TextFormat.simpleReplace(path, "/./", "/");
int pt = path.lastIndexOf("//") + 1;
@@ -705,7 +850,7 @@
return protocol + path;
}
- public String getFullPath(String name, boolean addUrlPrefix) {
+ String getFullPath(String name, boolean addUrlPrefix) {
String[] names = classifyName(name, false);
return (names == null ? "" : addUrlPrefix ? names[2] : names[0].replace(
'\\', '/'));
@@ -766,159 +911,6 @@
return (dir == null ? file : fixPath(dir.toString() + "/" + file));
}
- private static String addDirectory(String defaultDirectory, String name) {
- if (defaultDirectory.length() == 0)
- return name;
- char ch = (name.length() > 0 ? name.charAt(0) : ' ');
- String s = defaultDirectory.toLowerCase();
- if ((s.endsWith(".zip") || s.endsWith(".tar")) && ch != '|' && ch != '/')
- defaultDirectory += "|";
- return defaultDirectory
- + (ch == '/'
- || ch == '/'
- || (ch = defaultDirectory.charAt(defaultDirectory.length() - 1)) == '|'
- || ch == '/' ? "" : "/") + name;
- }
-
- Object getInputStreamOrErrorMessageFromName(String name, boolean showMsg) {
- String errorMessage = null;
- int iurlPrefix;
- for (iurlPrefix = urlPrefixes.length; --iurlPrefix >= 0;)
- if (name.startsWith(urlPrefixes[iurlPrefix]))
- break;
- boolean isURL = (iurlPrefix >= 0);
- boolean isApplet = (appletDocumentBase != null);
- InputStream in = null;
- //int length;
- try {
- if (isApplet || isURL) {
- if (isApplet && isURL && appletProxy != null)
- name = appletProxy + "?url=" + URLEncoder.encode(name, "utf-8");
- URL url = (isApplet ? new URL(appletDocumentBase, name) : new URL(name));
- name = url.toString();
- if (showMsg)
- Logger.info("FileManager opening " + url.toString());
- URLConnection conn = url.openConnection();
- //length = conn.getContentLength();
- in = conn.getInputStream();
- } else {
- if (showMsg)
- Logger.info("FileManager opening " + name);
- File file = new File(name);
- //length = (int) file.length();
- in = new FileInputStream(file);
- }
- return in;
- } catch (Exception e) {
- try {
- if (in != null)
- in.close();
- } catch (IOException e1) {
- }
- errorMessage = "" + e;
- }
- return errorMessage;
- }
-
- static BufferedReader getBufferedReaderForString(String string) {
- return new BufferedReader(new StringReader(string));
- }
-
- Object getBufferedReaderOrErrorMessageFromName(String name,
- String[] fullPathNameReturn,
- boolean isBinary, boolean doSpecialLoad) {
- String[] names = classifyName(name, true);
- if (names == null)
- return "cannot read file name: " + name;
- if (fullPathNameReturn != null)
- fullPathNameReturn[0] = names[0].replace('\\', '/');
- return getUnzippedBufferedReaderOrErrorMessageFromName(names[0], false,
- isBinary, false, doSpecialLoad);
- }
-
- Object getUnzippedBufferedReaderOrErrorMessageFromName(
- String name,
- boolean allowZipStream,
- boolean asInputStream,
- boolean isTypeCheckOnly, boolean doSpecialLoad) {
- String[] subFileList = null;
- String[] info = (doSpecialLoad ? viewer.getModelAdapter().specialLoad(name, "filesNeeded?") : null);
- if (info != null) {
- if (isTypeCheckOnly)
- return info;
- if (info[2] != null) {
- String header = info[1];
- Hashtable fileData = new Hashtable();
- if (info.length == 3) {
- // we need information from the output file, info[2]
- String name0 = getObjectAsSections(info[2], header, fileData);
- fileData.put("OUTPUT", name0);
- info = viewer.getModelAdapter().specialLoad(name,
- (String) fileData.get(name0));
- if (info.length == 3) {
- // might have a second option
- name0 = getObjectAsSections(info[2], header, fileData);
- fileData.put("OUTPUT", name0);
- info = viewer.getModelAdapter().specialLoad(info[1],
- (String) fileData.get(name0));
- }
- }
- return getBufferedReaderForString(getObjectAsSections(info, fileData));
- }
- // continuing...
- // here, for example, for an SPT file load that is not just a type check
- // (type check is only for application file opening and drag-drop to
- // determine if
- // script or load command should be used)
- }
- if (name.indexOf("|") >= 0)
- name = (subFileList = TextFormat.split(name, "|"))[0];
- Object t = getInputStreamOrErrorMessageFromName(name, true);
- if (t instanceof String)
- return t;
- try {
- BufferedInputStream bis = new BufferedInputStream((InputStream) t, 8192);
- InputStream is = bis;
- if (CompoundDocument.isCompoundDocument(is)) {
- CompoundDocument doc = new CompoundDocument(bis);
- return getBufferedReaderForString(doc.getAllData("Molecule").toString());
- } else if (ZipUtil.isGzip(is)) {
- do {
- is = new BufferedInputStream(new GZIPInputStream(is));
- } while (ZipUtil.isGzip(is));
- } else if (ZipUtil.isZipFile(is)) {
- if (allowZipStream)
- return new ZipInputStream(bis);
- if (asInputStream)
- return (InputStream) ZipUtil.getZipFileContents(is, subFileList, 1,
- true);
- // danger -- converting bytes to String here.
- // we lose 128-156 or so.
- String s = (String) ZipUtil.getZipFileContents(is, subFileList, 1,
- false);
- is.close();
- return getBufferedReaderForString(s);
- }
- if (asInputStream)
- return is;
- return new BufferedReader(new InputStreamReader(is));
- } catch (Exception ioe) {
- return ioe.getMessage();
- }
- }
-
- String[] getZipDirectory(String fileName, boolean addManifest) {
- return ZipUtil.getZipDirectoryAndClose(
- (InputStream) getInputStreamOrErrorMessageFromName(fileName, false),
- addManifest);
- }
-
- String getZipDirectoryAsString(String fileName) {
- return ZipUtil
- .getZipDirectoryAsStringAndClose((InputStream) getInputStreamOrErrorMessageFromName(
- fileName, false));
- }
-
/**
* Sets all local file references in a script file to point to files within
* dataPath. If a file reference contains dataPath, then the file reference is
@@ -963,7 +955,7 @@
return TextFormat.replaceQuotedStrings(script, fileNames, newFileNames);
}
- static String[] scriptFilePrefixes = new String[] { "/*file*/", "FILE0=", "FILE1=" };
+ private static String[] scriptFilePrefixes = new String[] { "/*file*/", "FILE0=", "FILE1=" };
public static void getFileReferences(String script, Vector fileList) {
for (int ipt = 0; ipt < scriptFilePrefixes.length; ipt++) {
String tag = scriptFilePrefixes[ipt];
Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-22 19:15:53 UTC (rev 11775)
+++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2009-11-22 19:16:27 UTC (rev 11776)
@@ -3,6 +3,8 @@
version=11.9.10_dev
+# bug fix: occasional null pointer error during ZAP due to continued rendering by
+# previous graphic painting thread
# code: refactoring of FileManager and clean-up of Viewer code
# in relation to model loading.
Modified: trunk/Jmol/src/org/jmol/viewer/MouseManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/MouseManager.java 2009-11-22 19:15:53 UTC (rev 11775)
+++ trunk/Jmol/src/org/jmol/viewer/MouseManager.java 2009-11-22 19:16:27 UTC (rev 11776)
@@ -45,6 +45,8 @@
}
void setActionManager(ActionManager actionManager) {
+ if (this.actionManager != null)
+ actionManager.clear();
this.actionManager = actionManager;
}
Modified: trunk/Jmol/src/org/jmol/viewer/RepaintManager.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/RepaintManager.java 2009-11-22 19:15:53 UTC (rev 11775)
+++ trunk/Jmol/src/org/jmol/viewer/RepaintManager.java 2009-11-22 19:16:27 UTC (rev 11776)
@@ -47,27 +47,22 @@
private int holdRepaint = 0;
boolean repaintPending;
+ private boolean repaintInterrupted = false;
void pushHoldRepaint() {
++holdRepaint;
}
void popHoldRepaint() {
- --holdRepaint;
- if (holdRepaint <= 0) {
- holdRepaint = 0;
- repaintPending = true;
+ if (--holdRepaint <= 0)
repaintDisplay();
- }
}
boolean refresh() {
if (repaintPending)
return false;
- repaintPending = true;
- if (holdRepaint == 0) {
+ if (holdRepaint == 0)
repaintDisplay();
- }
return true;
}
@@ -80,12 +75,28 @@
}
private void repaintDisplay() {
+ holdRepaint = 0;
+ repaintPending = true;
+ repaintInterrupted = false;
Component display = viewer.getDisplay();
if (display == null)
return;
display.repaint();
}
+ synchronized void cancelRendering() {
+ if (!repaintPending || repaintInterrupted)
+ return;
+ repaintInterrupted = true;
+ try {
+ //System.out.println("repaintManager waiting for rendering to complete");
+ wait();
+ } catch (InterruptedException e) {
+ }
+ repaintInterrupted = false;
+ //System.out.println("repaintManager continuing");
+ }
+
synchronized void repaintDone() {
repaintPending = false;
notify(); // to cancel any wait in requestRepaintAndWait()
@@ -94,17 +105,19 @@
void render(Graphics3D g3d, ModelSet modelSet) {// , Rectangle rectClip
if (!viewer.getRefreshing())
return;
- render1(g3d, modelSet); // , rectClip
- Rectangle band = viewer.getRubberBandSelection();
- if (band != null && g3d.setColix(viewer.getColixRubberband()))
- g3d.drawRect(band.x, band.y, 0, 0, band.width, band.height);
+ try {
+ render1(g3d, modelSet); // , rectClip
+ } catch (Exception e) {
+ System.out.println("rendering Exception " + e.getMessage());
+ }
}
private boolean logTime;
private void render1(Graphics3D g3d, ModelSet modelSet) { // , Rectangle rectClip
- if (modelSet == null || !viewer.mustRenderFlag())
+ if (modelSet == null || !viewer.mustRenderFlag()
+ || repaintInterrupted)
return;
logTime = viewer.getTestFlag1();
@@ -118,12 +131,19 @@
g3d.renderBackground();
if (renderers == null)
renderers = new ShapeRenderer[JmolConstants.SHAPE_MAX];
- for (int i = 0; i < JmolConstants.SHAPE_MAX && g3d.currentlyRendering(); ++i) {
+ for (int i = 0; i < JmolConstants.SHAPE_MAX
+ && g3d.currentlyRendering(); ++i) {
+ if (repaintInterrupted)
+ return;
Shape shape = modelSet.getShape(i);
if (shape == null)
continue;
+ //System.out.println("rendering " + JmolConstants.getShapeClassName(i));
getRenderer(i, g3d).render(g3d, modelSet, shape);
}
+ Rectangle band = viewer.getRubberBandSelection();
+ if (band != null && g3d.setColix(viewer.getColixRubberband()))
+ g3d.drawRect(band.x, band.y, 0, 0, band.width, band.height);
} catch (Exception e) {
Logger
Modified: trunk/Jmol/src/org/jmol/viewer/Viewer.java
===================================================================
--- trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-22 19:15:53 UTC (rev 11775)
+++ trunk/Jmol/src/org/jmol/viewer/Viewer.java 2009-11-22 19:16:27 UTC (rev 11776)
@@ -1663,20 +1663,15 @@
return global.defaultDirectory;
}
- public Object getBufferedReaderForString(String sdata) {
- return FileManager.getBufferedReaderForString(sdata);
- }
-
public BufferedInputStream getBufferedInputStream(String fullPathName) {
- Object ret = getBufferedReaderOrErrorMessageFromName(fullPathName,
- new String[2], true);
- return (ret instanceof BufferedInputStream ? (BufferedInputStream) ret
- : null);
+ // used by some JVXL readers
+ return fileManager.getBufferedInputStream(fullPathName);
}
public Object getBufferedReaderOrErrorMessageFromName(String name,
String[] fullPathNameReturn,
boolean isBinary) {
+ // used by isosurface reader
return fileManager.getBufferedReaderOrErrorMessageFromName(name,
fullPathNameReturn, isBinary, true);
}
@@ -2006,7 +2001,7 @@
private String openStringInline(String strModel, Hashtable htParams,
boolean isAppend) {
- // loadInline, openFile, openStringInline
+ // loadInline, openStringInline
if (!isAppend)
zap(true, false);
Object atomSetCollection = fileManager.createAtomSetCollectionFromString(strModel,
@@ -2016,7 +2011,7 @@
private String openStringsInline(String[] arrayModels, Hashtable htParams,
boolean isAppend) {
- // loadInline, openFile, openStringInline
+ // loadInline
if (!isAppend)
zap(true, false);
Object atomSetCollection = fileManager.createAtomSeCollectionFromStrings(arrayModels,
@@ -3413,7 +3408,7 @@
statusManager.setSync(null);
}
- public void repaintView() {
+ public void notifyViewerRepaintDone() {
repaintManager.repaintDone();
}
@@ -3550,7 +3545,7 @@
render1(gRight, getImage(true), 0, 0);
render1(gLeft, getImage(false), 0, 0);
}
- repaintView();
+ notifyViewerRepaintDone();
}
public void renderScreenImage(Graphics g, Dimension size, Rectangle clip) {
@@ -6279,6 +6274,7 @@
setSpinOn(false);
setNavOn(false);
setAnimationOn(false);
+ repaintManager.cancelRendering();
}
private void setNavigationMode(boolean TF) {
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