X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjavascript%2FMouseOverStructureListener.java;h=8d83e75300f84e7cf0cb6a59b01ea31b40d24a27;hb=9ae61a06b581ffba65614a2f08acc36e7f7685e7;hp=7f833e7fa4e0887b6350d952ad990c6c92c72ac2;hpb=088cd0cc2ea8c0ca326da400c2290d0fa759cdbb;p=jalview.git diff --git a/src/jalview/javascript/MouseOverStructureListener.java b/src/jalview/javascript/MouseOverStructureListener.java index 7f833e7..8d83e75 100644 --- a/src/jalview/javascript/MouseOverStructureListener.java +++ b/src/jalview/javascript/MouseOverStructureListener.java @@ -30,12 +30,9 @@ import jalview.ext.jmol.JmolCommands; import jalview.structure.AtomSpec; import jalview.structure.StructureListener; import jalview.structure.StructureMapping; -import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; +import jalview.util.HttpUtils; -import java.io.IOException; -import java.io.InputStream; -import java.net.URL; import java.util.ArrayList; import java.util.List; @@ -72,8 +69,8 @@ import java.util.List; * @author Jim Procter (jprocter) * */ -public class MouseOverStructureListener extends JSFunctionExec implements - JsCallBack, StructureListener +public class MouseOverStructureListener extends JSFunctionExec + implements JsCallBack, StructureListener { String _listenerfn; @@ -90,14 +87,13 @@ public class MouseOverStructureListener extends JSFunctionExec implements { for (int i = 0; i < modelSet.length; i++) { - // ? leave file names 'as is' to match StructureMapping.pdbfile - // modelSet[i] = resolveModelFile(modelSet[i]); + modelSet[i] = resolveModelFile(modelSet[i]); } } } /** - * Returns the first out of file, file prefixed by document base, or file + * Returns the first out of: file, file prefixed by document base, or file * prefixed by codebase which can be resolved to a valid URL. If none can, * returns the input parameter value. * @@ -105,7 +101,8 @@ public class MouseOverStructureListener extends JSFunctionExec implements */ public String resolveModelFile(String file) { - if (isValidUrl(file)) + // TODO reuse JalviewLite.LoadingThread.addProtocol instead + if (HttpUtils.isValidUrl(file)) { return file; } @@ -113,13 +110,13 @@ public class MouseOverStructureListener extends JSFunctionExec implements String db = jvlite.getDocumentBase().toString(); db = db.substring(0, db.lastIndexOf("/")); String docBaseFile = db + "/" + file; - if (isValidUrl(docBaseFile)) + if (HttpUtils.isValidUrl(docBaseFile)) { return docBaseFile; } String cb = jvlite.getCodeBase() + file; - if (isValidUrl(cb)) + if (HttpUtils.isValidUrl(cb)) { return cb; } @@ -127,45 +124,8 @@ public class MouseOverStructureListener extends JSFunctionExec implements return file; } - /** - * Returns true if it is possible to open an input stream at the given URL, - * else false. The input stream is closed. - * - * @param file - * @return - */ - private boolean isValidUrl(String file) - { - InputStream is = null; - try - { - is = new URL(file).openStream(); - if (is != null) - { - return true; - } - } catch (IOException x) - { - // MalformedURLException, FileNotFoundException - return false; - } finally - { - if (is != null) - { - try - { - is.close(); - } catch (IOException e) - { - // ignore - } - } - } - return false; - } - @Override - public String[] getPdbFile() + public String[] getStructureFiles() { return modelSet; } @@ -191,9 +151,9 @@ public class MouseOverStructureListener extends JSFunctionExec implements // JBPComment: yep - this is right! the Javascript harness uses the // absolute pdbFile URI to locate the PDB file in the external viewer executeJavascriptFunction(_listenerfn, - new String[] { "mouseover", "" + atom.getPdbFile(), - "" + atom.getChain(), "" + (atom.getPdbResNum()), - "" + atom.getAtomIndex() }); + new String[] + { "mouseover", "" + atom.getPdbFile(), "" + atom.getChain(), + "" + (atom.getPdbResNum()), "" + atom.getAtomIndex() }); } catch (Exception ex) { System.err.println("Couldn't execute callback with " + _listenerfn @@ -212,8 +172,8 @@ public class MouseOverStructureListener extends JSFunctionExec implements if (JalviewLite.debug) { - System.err.println(this.getClass().getName() + " modelSet[0]: " - + modelSet[0]); + System.err.println( + this.getClass().getName() + " modelSet[0]: " + modelSet[0]); ssm.reportMapping(); } @@ -245,33 +205,36 @@ public class MouseOverStructureListener extends JSFunctionExec implements SequenceRenderer sr = ((jalview.appletgui.AlignmentPanel) source) .getSequenceRenderer(); FeatureRenderer fr = ((jalview.appletgui.AlignmentPanel) source).av - .isShowSequenceFeatures() ? new jalview.appletgui.FeatureRenderer( - ((jalview.appletgui.AlignmentPanel) source).av) : null; + .isShowSequenceFeatures() + ? new jalview.appletgui.FeatureRenderer( + ((jalview.appletgui.AlignmentPanel) source).av) + : null; if (fr != null) { - ((jalview.appletgui.FeatureRenderer) fr) - .transferSettings(((jalview.appletgui.AlignmentPanel) source) + ((jalview.appletgui.FeatureRenderer) fr).transferSettings( + ((jalview.appletgui.AlignmentPanel) source) .getFeatureRenderer()); } ; // Form a colour command from the given alignment panel for each distinct // structure - ArrayList ccomands = new ArrayList(); - ArrayList pdbfn = new ArrayList(); - StructureMappingcommandSet[] colcommands = JmolCommands - .getColourBySequenceCommand(ssm, modelSet, sequence, sr, fr, - ((AlignmentViewPanel) source).getAlignment()); + ArrayList ccomands = new ArrayList<>(); + ArrayList pdbfn = new ArrayList<>(); + String[] colcommands = new JmolCommands() + .colourBySequence(ssm, modelSet, sequence, sr, + (AlignmentViewPanel) source); if (colcommands == null) { return; } int sz = 0; - for (jalview.structure.StructureMappingcommandSet ccset : colcommands) + // for (jalview.structure.StructureMappingcommandSet ccset : colcommands) + for (String command : colcommands) { - sz += ccset.commands.length; - ccomands.add(ccset.commands); - pdbfn.add(ccset.mapping); + // sz += ccset.commands.length; + // ccomands.add(command); // ccset.commands); + // pdbfn.add(ccset.mapping); } String mclass, mhandle; @@ -282,27 +245,25 @@ public class MouseOverStructureListener extends JSFunctionExec implements System.arraycopy(ccset, 0, ccomandset, sz, ccset.length); sz += ccset.length; } - if (jvlite.isJsMessageSetChanged( - mclass = "colourstruct", + if (jvlite.isJsMessageSetChanged(mclass = "colourstruct", mhandle = ((jalview.appletgui.AlignmentPanel) source).av - .getViewId(), ccomandset)) + .getViewId(), + ccomandset)) { jvlite.setJsMessageSet(mclass, mhandle, ccomandset); // and notify javascript handler - String st[] = new String[] { - "colourstruct", + String st[] = new String[] { "colourstruct", "" + ((jalview.appletgui.AlignmentPanel) source).av.getViewId(), - "" + ccomandset.length, - jvlite.arrayToSeparatorList(pdbfn.toArray(new String[pdbfn - .size()])) }; + "" + ccomandset.length, jvlite.arrayToSeparatorList( + pdbfn.toArray(new String[pdbfn.size()])) }; try { executeJavascriptFunction(true, _listenerfn, st); } catch (Exception ex) { - System.err.println("Couldn't execute callback with " - + _listenerfn + " using args { " + st[0] + ", " + st[1] - + ", " + st[2] + "," + st[3] + "}"); // + ","+st[4]+"\n"); + System.err.println("Couldn't execute callback with " + _listenerfn + + " using args { " + st[0] + ", " + st[1] + ", " + st[2] + + "," + st[3] + "}"); // + ","+st[4]+"\n"); ex.printStackTrace(); } @@ -337,12 +298,6 @@ public class MouseOverStructureListener extends JSFunctionExec implements return _listenerfn; } - public void finalise() - { - jvlite = null; - super.finalize(); - } - @Override public void releaseReferences(Object svl) {