X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=c2a7299d66a176a36d722a794166421d507c21e9;hb=3412b273e964fb1a9d22564b04a5f0c827ec2461;hp=4dfd18a0e08ccd158b6e28c79d9b260ef0c1ab41;hpb=cca50cb3aee94f3ed1a5e504d45b8d8b665f8c5b;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 4dfd18a..c2a7299 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,34 +20,8 @@ */ package jalview.gui; -import jalview.api.structures.JalviewStructureDisplayI; -import jalview.bin.Cache; -import jalview.datamodel.Alignment; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.ext.jmol.JalviewJmolBinding; -import jalview.gui.ViewSelectionMenu.ViewSetProvider; -import jalview.io.AppletFormatAdapter; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.jbgui.GStructureViewer; -import jalview.schemes.BuriedColourScheme; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.HelixColourScheme; -import jalview.schemes.HydrophobicColourScheme; -import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.StrandColourScheme; -import jalview.schemes.TaylorColourScheme; -import jalview.schemes.TurnColourScheme; -import jalview.schemes.ZappoColourScheme; -import jalview.util.MessageManager; -import jalview.util.Platform; - import java.awt.BorderLayout; import java.awt.Color; -import java.awt.Component; import java.awt.Dimension; import java.awt.Font; import java.awt.Graphics; @@ -61,7 +35,6 @@ import java.io.File; import java.io.FileOutputStream; import java.io.FileReader; import java.io.PrintWriter; -import java.util.ArrayList; import java.util.Enumeration; import java.util.Vector; @@ -78,9 +51,30 @@ import javax.swing.event.InternalFrameEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; -public class AppJmol extends GStructureViewer implements Runnable, - ViewSetProvider, JalviewStructureDisplayI +import jalview.bin.Cache; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.gui.StructureViewer.ViewerType; +import jalview.io.AppletFormatAdapter; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.PurinePyrimidineColourScheme; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.ZappoColourScheme; +import jalview.structures.models.AAStructureBindingModel; +import jalview.util.MessageManager; +import jalview.util.Platform; +public class AppJmol extends StructureViewerBase { AppJmolBinding jmb; @@ -90,8 +84,6 @@ public class AppJmol extends GStructureViewer implements Runnable, RenderPanel renderPanel; - AlignmentPanel ap; - Vector atomsPicked = new Vector(); private boolean addingStructures = false; @@ -156,9 +148,9 @@ public class AppJmol extends GStructureViewer implements Runnable, PDBEntry[] pdbentrys = new PDBEntry[files.length]; for (int i = 0; i < pdbentrys.length; i++) { - PDBEntry pdbentry = new PDBEntry(); - pdbentry.setFile(files[i]); - pdbentry.setId(ids[i]); + // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]); + PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB, + files[i]); pdbentrys[i] = pdbentry; } // / TODO: check if protocol is needed to be set, and if chains are @@ -178,7 +170,7 @@ public class AppJmol extends GStructureViewer implements Runnable, seqColour.setSelected(false); viewerColour.setSelected(true); } - if (usetoColour) + else if (usetoColour) { useAlignmentPanelForColourbyseq(ap); jmb.setColourBySequence(true); @@ -187,7 +179,7 @@ public class AppJmol extends GStructureViewer implements Runnable, } this.setBounds(bounds); initMenus(); - viewId = viewid; + setViewId(viewid); // jalview.gui.Desktop.addInternalFrame(this, "Loading File", // bounds.width,bounds.height); @@ -195,7 +187,7 @@ public class AppJmol extends GStructureViewer implements Runnable, { public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); initJmol(loadStatus); // pdbentry, seq, JBPCHECK! @@ -332,15 +324,16 @@ public class AppJmol extends GStructureViewer implements Runnable, final AppJmol topJmol = ((AppJmol) frames[i]); // JBPNOTE: this looks like a binding routine, rather than a gui // routine - for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++) + for (int pe = 0; pe < topJmol.jmb.getPdbCount(); pe++) { - if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped)) + if (topJmol.jmb.getPdbEntry(pe).getFile() + .equals(alreadyMapped)) { topJmol.jmb.addSequence(pe, seq); topJmol.addAlignmentPanel(ap); // add it to the set used for colouring topJmol.useAlignmentPanelForColourbyseq(ap); - topJmol.buildJmolActionMenu(); + topJmol.buildActionMenu(); ap.getStructureSelectionManager() .sequenceColoursChanged(ap); break; @@ -416,7 +409,7 @@ public class AppJmol extends GStructureViewer implements Runnable, { public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); @@ -436,133 +429,6 @@ public class AppJmol extends GStructureViewer implements Runnable, } /** - * list of sequenceSet ids associated with the view - */ - ArrayList _aps = new ArrayList(); - - public AlignmentPanel[] getAllAlignmentPanels() - { - AlignmentPanel[] t, list = new AlignmentPanel[0]; - for (String setid : _aps) - { - AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid); - if (panels != null) - { - t = new AlignmentPanel[list.length + panels.length]; - System.arraycopy(list, 0, t, 0, list.length); - System.arraycopy(panels, 0, t, list.length, panels.length); - list = t; - } - } - - return list; - } - - /** - * list of alignment panels to use for superposition - */ - Vector _alignwith = new Vector(); - - /** - * list of alignment panels that are used for colouring structures by aligned - * sequences - */ - Vector _colourwith = new Vector(); - - /** - * set the primary alignmentPanel reference and add another alignPanel to the - * list of ones to use for colouring and aligning - * - * @param nap - */ - public void addAlignmentPanel(AlignmentPanel nap) - { - if (ap == null) - { - ap = nap; - } - if (!_aps.contains(nap.av.getSequenceSetId())) - { - _aps.add(nap.av.getSequenceSetId()); - } - } - - /** - * remove any references held to the given alignment panel - * - * @param nap - */ - public void removeAlignmentPanel(AlignmentPanel nap) - { - try - { - _alignwith.remove(nap); - _colourwith.remove(nap); - if (ap == nap) - { - ap = null; - for (AlignmentPanel aps : getAllAlignmentPanels()) - { - if (aps != nap) - { - ap = aps; - break; - } - } - } - } catch (Exception ex) - { - } - if (ap != null) - { - buildJmolActionMenu(); - } - } - - public void useAlignmentPanelForSuperposition(AlignmentPanel nap) - { - addAlignmentPanel(nap); - if (!_alignwith.contains(nap)) - { - _alignwith.add(nap); - } - } - - public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap) - { - if (_alignwith.contains(nap)) - { - _alignwith.remove(nap); - } - } - - public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, - boolean enableColourBySeq) - { - useAlignmentPanelForColourbyseq(nap); - jmb.setColourBySequence(enableColourBySeq); - seqColour.setSelected(enableColourBySeq); - viewerColour.setSelected(!enableColourBySeq); - } - - public void useAlignmentPanelForColourbyseq(AlignmentPanel nap) - { - addAlignmentPanel(nap); - if (!_colourwith.contains(nap)) - { - _colourwith.add(nap); - } - } - - public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap) - { - if (_colourwith.contains(nap)) - { - _colourwith.remove(nap); - } - } - - /** * pdb retrieval thread. */ private Thread worker = null; @@ -632,7 +498,7 @@ public class AppJmol extends GStructureViewer implements Runnable, { if (frame instanceof AppJmol) { - if (((AppJmol) frame).isLinkedWith(apanel)) + if (((StructureViewerBase) frame).isLinkedWith(apanel)) { result.addElement(frame); } @@ -739,10 +605,11 @@ public class AppJmol extends GStructureViewer implements Runnable, jmb.centerViewer(toshow); } - public void closeViewer() + public void closeViewer(boolean closeExternalViewer) { + // JMol does not use an external viewer jmb.closeViewer(); - ap = null; + setAlignmentPanel(null); _aps.clear(); _alignwith.clear(); _colourwith.clear(); @@ -768,14 +635,14 @@ public class AppJmol extends GStructureViewer implements Runnable, // TODO: replace with reference fetching/transfer code (validate PDBentry // as a DBRef?) jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb(); - for (int pi = 0; pi < jmb.pdbentry.length; pi++) + for (int pi = 0; pi < jmb.getPdbCount(); pi++) { - String file = jmb.pdbentry[pi].getFile(); + String file = jmb.getPdbEntry(pi).getFile(); if (file == null) { // retrieve the pdb and store it locally AlignmentI pdbseq = null; - pdbid = jmb.pdbentry[pi].getId(); + pdbid = jmb.getPdbEntry(pi).getId(); long hdl = pdbid.hashCode() - System.currentTimeMillis(); if (progressBar != null) { @@ -783,8 +650,7 @@ public class AppJmol extends GStructureViewer implements Runnable, } try { - pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi] - .getId()); + pdbseq = pdbclient.getSequenceRecords(pdbid); } catch (OutOfMemoryError oomerror) { new OOMWarning("Retrieving PDB id " + pdbid, oomerror); @@ -801,9 +667,9 @@ public class AppJmol extends GStructureViewer implements Runnable, { // just transfer the file name from the first sequence's first // PDBEntry - file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId() - .elementAt(0)).getFile()).getAbsolutePath(); - jmb.pdbentry[pi].setFile(file); + file = new File(pdbseq.getSequenceAt(0).getPDBId() + .elementAt(0).getFile()).getAbsolutePath(); + jmb.getPdbEntry(pi).setFile(file); files.append(" \"" + Platform.escapeString(file) + "\""); } @@ -898,7 +764,7 @@ public class AppJmol extends GStructureViewer implements Runnable, // need to wait around until script has finished while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() : (jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb - .getPdbFile().length != jmb.pdbentry.length)) + .getPdbFile().length != jmb.getPdbCount())) { try { @@ -977,11 +843,7 @@ public class AppJmol extends GStructureViewer implements Runnable, jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); try { - for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++) - { - cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile())); - cap.appendText("\n"); - } + cap.appendText(jmb.printMappings()); } catch (OutOfMemoryError e) { new OOMWarning( @@ -1065,16 +927,16 @@ public class AppJmol extends GStructureViewer implements Runnable, { if (!jmb.isLoadingFromArchive()) { - if (_colourwith.size() == 0 && ap != null) + if (_colourwith.size() == 0 && getAlignmentPanel() != null) { // Make the currently displayed alignment panel the associated view - _colourwith.add(ap.alignFrame.alignPanel); + _colourwith.add(getAlignmentPanel().alignFrame.alignPanel); } } // Set the colour using the current view for the associated alignframe for (AlignmentPanel ap : _colourwith) { - jmb.colourBySequence(ap.av.showSequenceFeatures, ap); + jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap); } } } @@ -1222,7 +1084,7 @@ public class AppJmol extends GStructureViewer implements Runnable, getSize(currentSize); g.getClipBounds(rectClip); - if (jmb.fileLoadingError != null) + if (jmb != null && jmb.fileLoadingError != null) { g.setColor(Color.black); g.fillRect(0, 0, currentSize.width, currentSize.height); @@ -1232,15 +1094,15 @@ public class AppJmol extends GStructureViewer implements Runnable, + "...", 20, currentSize.height / 2); StringBuffer sb = new StringBuffer(); int lines = 0; - for (int e = 0; e < jmb.pdbentry.length; e++) + for (int e = 0; e < jmb.getPdbCount(); e++) { - sb.append(jmb.pdbentry[e].getId()); - if (e < jmb.pdbentry.length - 1) + sb.append(jmb.getPdbEntry(e).getId()); + if (e < jmb.getPdbCount() - 1) { sb.append(","); } - if (e == jmb.pdbentry.length - 1 || sb.length() > 20) + if (e == jmb.getPdbCount() - 1 || sb.length() > 20) { lines++; g.drawString(sb.toString(), 20, currentSize.height / 2 - lines @@ -1264,17 +1126,6 @@ public class AppJmol extends GStructureViewer implements Runnable, } } - String viewId = null; - - public String getViewId() - { - if (viewId == null) - { - viewId = System.currentTimeMillis() + "." + this.hashCode(); - } - return viewId; - } - public void updateTitleAndMenus() { if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) @@ -1285,7 +1136,7 @@ public class AppJmol extends GStructureViewer implements Runnable, setChainMenuItems(jmb.chainNames); this.setTitle(jmb.getViewerTitle()); - if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1) + if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1) { viewerActionMenu.setVisible(true); } @@ -1295,27 +1146,6 @@ public class AppJmol extends GStructureViewer implements Runnable, } } - protected void buildJmolActionMenu() - { - if (_alignwith == null) - { - _alignwith = new Vector(); - } - if (_alignwith.size() == 0 && ap != null) - { - _alignwith.add(ap); - } - ; - for (Component c : viewerActionMenu.getMenuComponents()) - { - if (c != alignStructs) - { - viewerActionMenu.remove((JMenuItem) c); - } - } - final ItemListener handler; - } - /* * (non-Javadoc) * @@ -1331,14 +1161,14 @@ public class AppJmol extends GStructureViewer implements Runnable, private void alignStructs_withAllAlignPanels() { - if (ap == null) + if (getAlignmentPanel() == null) { return; } ; if (_alignwith.size() == 0) { - _alignwith.add(ap); + _alignwith.add(getAlignmentPanel()); } ; try @@ -1390,42 +1220,25 @@ public class AppJmol extends GStructureViewer implements Runnable, return ap; } } - return ap; - } - - /** - * - * @param ap2 - * @return true if this Jmol instance is linked with the given alignPanel - */ - public boolean isLinkedWith(AlignmentPanel ap2) - { - return _aps.contains(ap2.av.getSequenceSetId()); - } - - public boolean isUsedforaligment(AlignmentPanel ap2) - { - - return (_alignwith != null) && _alignwith.contains(ap2); + return getAlignmentPanel(); } - public boolean isUsedforcolourby(AlignmentPanel ap2) + @Override + public AAStructureBindingModel getBinding() { - return (_colourwith != null) && _colourwith.contains(ap2); + return this.jmb; } - /** - * - * @return TRUE if the view is NOT being coloured by sequence associations. - */ - public boolean isColouredByJmol() + @Override + public String getStateInfo() { - return !jmb.isColourBySequence(); + return jmb == null ? null : jmb.viewer.getStateInfo(); } - public JalviewJmolBinding getBinding() + @Override + public ViewerType getViewerType() { - return jmb; + return ViewerType.JMOL; } }