X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=90d3b153c190c99fd9e8c008c96071ae0c195f75;hb=c66902a9536b10a5477b58aaf7c2d75772890a5d;hp=6eb6ac333302c721983ad16f0cd6677e9e3f5fd0;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 6eb6ac3..90d3b15 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -20,27 +20,64 @@ */ package jalview.gui; -import java.util.*; -import java.awt.*; -import javax.swing.*; -import javax.swing.event.*; - -import java.awt.event.*; -import java.io.*; - -import jalview.jbgui.GStructureViewer; -import jalview.api.SequenceStructureBinding; import jalview.bin.Cache; -import jalview.datamodel.*; -import jalview.gui.ViewSelectionMenu.ViewSetProvider; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; -import jalview.io.*; -import jalview.schemes.*; +import jalview.datamodel.SequenceI; +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.structures.models.AAStructureBindingModel; 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; +import java.awt.Rectangle; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.io.BufferedReader; +import java.io.File; +import java.io.FileOutputStream; +import java.io.FileReader; +import java.io.PrintWriter; +import java.util.Enumeration; +import java.util.Vector; + +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JColorChooser; +import javax.swing.JInternalFrame; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.JPanel; +import javax.swing.JSplitPane; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; +import javax.swing.event.MenuEvent; +import javax.swing.event.MenuListener; + public class AppJmol extends GStructureViewer implements Runnable, - SequenceStructureBinding, ViewSetProvider + ViewSetProvider { AppJmolBinding jmb; @@ -67,6 +104,7 @@ public class AppJmol extends GStructureViewer implements Runnable, * @param bounds * @deprecated defaults to AppJmol(String[] files, ... , viewid); */ + @Deprecated public AppJmol(String file, String id, SequenceI[] seq, AlignmentPanel ap, String loadStatus, Rectangle bounds) { @@ -76,6 +114,7 @@ public class AppJmol extends GStructureViewer implements Runnable, /** * @deprecated */ + @Deprecated public AppJmol(String file, String id, SequenceI[] seq, AlignmentPanel ap, String loadStatus, Rectangle bounds, String viewid) @@ -135,18 +174,18 @@ public class AppJmol extends GStructureViewer implements Runnable, { jmb.setColourBySequence(false); seqColour.setSelected(false); - jmolColour.setSelected(true); + viewerColour.setSelected(true); } if (usetoColour) { useAlignmentPanelForColourbyseq(ap); jmb.setColourBySequence(true); seqColour.setSelected(true); - jmolColour.setSelected(false); + viewerColour.setSelected(false); } this.setBounds(bounds); initMenus(); - viewId = viewid; + setViewId(viewid); // jalview.gui.Desktop.addInternalFrame(this, "Loading File", // bounds.width,bounds.height); @@ -164,7 +203,7 @@ public class AppJmol extends GStructureViewer implements Runnable, private void initMenus() { seqColour.setSelected(jmb.isColourBySequence()); - jmolColour.setSelected(!jmb.isColourBySequence()); + viewerColour.setSelected(!jmb.isColourBySequence()); if (_colourwith == null) { _colourwith = new Vector(); @@ -174,7 +213,7 @@ public class AppJmol extends GStructureViewer implements Runnable, _alignwith = new Vector(); } - seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith, + seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith, new ItemListener() { @@ -194,7 +233,7 @@ public class AppJmol extends GStructureViewer implements Runnable, }); viewMenu.add(seqColourBy); final ItemListener handler; - JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this, + JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this, _alignwith, handler = new ItemListener() { @@ -210,8 +249,8 @@ public class AppJmol extends GStructureViewer implements Runnable, } }); handler.itemStateChanged(null); - jmolActionMenu.add(alpanels); - jmolActionMenu.addMenuListener(new MenuListener() + viewerActionMenu.add(alpanels); + viewerActionMenu.addMenuListener(new MenuListener() { @Override @@ -262,16 +301,21 @@ public class AppJmol extends GStructureViewer implements Runnable, "label.pdb_entry_is_already_displayed", new String[] { pdbentry.getId() }), MessageManager.formatMessage( "label.map_sequences_to_visible_window", new String[] - { pdbentry.getId() }), JOptionPane.YES_NO_OPTION); + { pdbentry.getId() }), + JOptionPane.YES_NO_CANCEL_OPTION); + if (option == JOptionPane.CANCEL_OPTION) + { + return; + } if (option == JOptionPane.YES_OPTION) { // TODO : Fix multiple seq to one chain issue here. ap.getStructureSelectionManager().setMapping(seq, chains, alreadyMapped, AppletFormatAdapter.FILE); - if (ap.seqPanel.seqCanvas.fr != null) + if (ap.getSeqPanel().seqCanvas.fr != null) { - ap.seqPanel.seqCanvas.fr.featuresAdded(); + ap.getSeqPanel().seqCanvas.fr.featuresAdded(); ap.paintAlignment(true); } @@ -286,9 +330,10 @@ 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); @@ -325,7 +370,11 @@ public class AppJmol extends GStructureViewer implements Runnable, { pdbentry.getId(), topJmol.getTitle() }), MessageManager .getString("label.align_to_existing_structure_view"), - JOptionPane.YES_NO_OPTION); + JOptionPane.YES_NO_CANCEL_OPTION); + if (option == JOptionPane.CANCEL_OPTION) + { + return; + } if (option == JOptionPane.YES_OPTION) { topJmol.useAlignmentPanelForSuperposition(ap); @@ -385,11 +434,6 @@ public class AppJmol extends GStructureViewer implements Runnable, openNewJmol(ap, pe, seqs); } - /** - * list of sequenceSet ids associated with the view - */ - ArrayList _aps = new ArrayList(); - public AlignmentPanel[] getAllAlignmentPanels() { AlignmentPanel[] t, list = new AlignmentPanel[0]; @@ -409,17 +453,6 @@ public class AppJmol extends GStructureViewer implements Runnable, } /** - * 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 * @@ -492,7 +525,7 @@ public class AppJmol extends GStructureViewer implements Runnable, useAlignmentPanelForColourbyseq(nap); jmb.setColourBySequence(enableColourBySeq); seqColour.setSelected(enableColourBySeq); - jmolColour.setSelected(!enableColourBySeq); + viewerColour.setSelected(!enableColourBySeq); } public void useAlignmentPanelForColourbyseq(AlignmentPanel nap) @@ -573,25 +606,22 @@ public class AppJmol extends GStructureViewer implements Runnable, return; } - private Vector getJmolsFor(AlignmentPanel ap2) + private Vector getJmolsFor(AlignmentPanel apanel) { - Vector otherJmols = new Vector(); - // Now this AppJmol is mapped to new sequences. We must add them to - // the exisiting array + Vector result = new Vector(); JInternalFrame[] frames = Desktop.instance.getAllFrames(); - for (int i = 0; i < frames.length; i++) + for (JInternalFrame frame : frames) { - if (frames[i] instanceof AppJmol) + if (frame instanceof AppJmol) { - AppJmol topJmol = ((AppJmol) frames[i]); - if (topJmol.isLinkedWith(ap2)) + if (((GStructureViewer) frame).isLinkedWith(apanel)) { - otherJmols.addElement(topJmol); + result.addElement(frame); } } } - return otherJmols; + return result; } void initJmol(String command) @@ -640,7 +670,9 @@ public class AppJmol extends GStructureViewer implements Runnable, for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) + { ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true); + } } centerViewer(); allChainsSelected = false; @@ -657,7 +689,9 @@ public class AppJmol extends GStructureViewer implements Runnable, public void itemStateChanged(ItemEvent evt) { if (!allChainsSelected) + { centerViewer(); + } } }); @@ -688,7 +722,7 @@ public class AppJmol extends GStructureViewer implements Runnable, jmb.centerViewer(toshow); } - void closeViewer() + public void closeViewer() { jmb.closeViewer(); ap = null; @@ -717,22 +751,23 @@ 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) { - progressBar.setProgressBar("Fetching PDB " + pdbid, hdl); + progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl); } try { - pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi] + pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.getPdbEntry( + pi) .getId()); } catch (OutOfMemoryError oomerror) { @@ -744,7 +779,7 @@ public class AppJmol extends GStructureViewer implements Runnable, } if (progressBar != null) { - progressBar.setProgressBar("Finished.", hdl); + progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl); } if (pdbseq != null) { @@ -752,7 +787,7 @@ public class AppJmol extends GStructureViewer implements Runnable, // PDBEntry file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId() .elementAt(0)).getFile()).getAbsolutePath(); - jmb.pdbentry[pi].setFile(file); + jmb.getPdbEntry(pi).setFile(file); files.append(" \"" + Platform.escapeString(file) + "\""); } @@ -847,7 +882,7 @@ 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 { @@ -882,13 +917,14 @@ public class AppJmol extends GStructureViewer implements Runnable, worker = null; } + @Override public void pdbFile_actionPerformed(ActionEvent actionEvent) { JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save PDB File"); + chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -919,14 +955,15 @@ public class AppJmol extends GStructureViewer implements Runnable, } } + @Override public void viewMapping_actionPerformed(ActionEvent actionEvent) { jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); try { - for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++) + for (int pdbe = 0; pdbe < jmb.getPdbCount(); pdbe++) { - cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile())); + cap.appendText(jmb.printMapping(jmb.getPdbEntry(pdbe).getFile())); cap.appendText("\n"); } } catch (OutOfMemoryError e) @@ -942,46 +979,45 @@ public class AppJmol extends GStructureViewer implements Runnable, 600); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ + @Override public void eps_actionPerformed(ActionEvent e) { - makePDBImage(jalview.util.ImageMaker.EPS); + makePDBImage(jalview.util.ImageMaker.TYPE.EPS); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ + @Override public void png_actionPerformed(ActionEvent e) { - makePDBImage(jalview.util.ImageMaker.PNG); + makePDBImage(jalview.util.ImageMaker.TYPE.PNG); } - void makePDBImage(int type) + void makePDBImage(jalview.util.ImageMaker.TYPE type) { int width = getWidth(); int height = getHeight(); jalview.util.ImageMaker im; - if (type == jalview.util.ImageMaker.PNG) + if (type == jalview.util.ImageMaker.TYPE.PNG) { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG, + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view", width, height, null, null); } - else + else if (type == jalview.util.ImageMaker.TYPE.EPS) { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view", width, height, null, this.getTitle()); } + else + { + + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA", + width, height, null, this.getTitle()); + } if (im.getGraphics() != null) { @@ -991,15 +1027,17 @@ public class AppJmol extends GStructureViewer implements Runnable, } } - public void jmolColour_actionPerformed(ActionEvent actionEvent) + @Override + public void viewerColour_actionPerformed(ActionEvent actionEvent) { - if (jmolColour.isSelected()) + if (viewerColour.isSelected()) { // disable automatic sequence colouring. jmb.setColourBySequence(false); } } + @Override public void seqColour_actionPerformed(ActionEvent actionEvent) { jmb.setColourBySequence(seqColour.isSelected()); @@ -1025,82 +1063,95 @@ public class AppJmol extends GStructureViewer implements Runnable, } } + @Override public void chainColour_actionPerformed(ActionEvent actionEvent) { chainColour.setSelected(true); jmb.colourByChain(); } + @Override public void chargeColour_actionPerformed(ActionEvent actionEvent) { chargeColour.setSelected(true); jmb.colourByCharge(); } + @Override public void zappoColour_actionPerformed(ActionEvent actionEvent) { zappoColour.setSelected(true); jmb.setJalviewColourScheme(new ZappoColourScheme()); } + @Override public void taylorColour_actionPerformed(ActionEvent actionEvent) { taylorColour.setSelected(true); jmb.setJalviewColourScheme(new TaylorColourScheme()); } + @Override public void hydroColour_actionPerformed(ActionEvent actionEvent) { hydroColour.setSelected(true); jmb.setJalviewColourScheme(new HydrophobicColourScheme()); } + @Override public void helixColour_actionPerformed(ActionEvent actionEvent) { helixColour.setSelected(true); jmb.setJalviewColourScheme(new HelixColourScheme()); } + @Override public void strandColour_actionPerformed(ActionEvent actionEvent) { strandColour.setSelected(true); jmb.setJalviewColourScheme(new StrandColourScheme()); } + @Override public void turnColour_actionPerformed(ActionEvent actionEvent) { turnColour.setSelected(true); jmb.setJalviewColourScheme(new TurnColourScheme()); } + @Override public void buriedColour_actionPerformed(ActionEvent actionEvent) { buriedColour.setSelected(true); jmb.setJalviewColourScheme(new BuriedColourScheme()); } + @Override public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) { setJalviewColourScheme(new PurinePyrimidineColourScheme()); } + @Override public void userColour_actionPerformed(ActionEvent actionEvent) { userColour.setSelected(true); new UserDefinedColours(this, null); } + @Override public void backGround_actionPerformed(ActionEvent actionEvent) { java.awt.Color col = JColorChooser.showDialog(this, - "Select Background Colour", null); + MessageManager.getString("label.select_backgroud_colour"), null); if (col != null) { jmb.setBackgroundColour(col); } } - public void jmolHelp_actionPerformed(ActionEvent actionEvent) + @Override + public void showHelp_actionPerformed(ActionEvent actionEvent) { try { @@ -1165,15 +1216,15 @@ 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 @@ -1197,17 +1248,6 @@ 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) @@ -1218,9 +1258,9 @@ 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) { - jmolActionMenu.setVisible(true); + viewerActionMenu.setVisible(true); } if (!jmb.isLoadingFromArchive()) { @@ -1239,11 +1279,11 @@ public class AppJmol extends GStructureViewer implements Runnable, _alignwith.add(ap); } ; - for (Component c : jmolActionMenu.getMenuComponents()) + for (Component c : viewerActionMenu.getMenuComponents()) { if (c != alignStructs) { - jmolActionMenu.remove((JMenuItem) c); + viewerActionMenu.remove((JMenuItem) c); } } final ItemListener handler; @@ -1326,34 +1366,16 @@ public class AppJmol extends GStructureViewer implements Runnable, 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); - } - - 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(); } }