X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=fcb31eb57504dc9c45e3060083abd1fe362b9f8f;hb=d3a2fdc864b586b5c604335dd715ec215b679197;hp=5d4b910304561e36be6d540bbe36f03505fb4542;hpb=9b748cf747fedad98cb9c1f4e2f9aaf565c176cb;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 5d4b910..fcb31eb 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -176,14 +176,14 @@ 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(); @@ -205,7 +205,7 @@ 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(); @@ -251,8 +251,8 @@ 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 @@ -303,8 +303,13 @@ 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. @@ -366,7 +371,11 @@ 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); @@ -533,7 +542,7 @@ 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) @@ -614,25 +623,22 @@ 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 (((AppJmol) frame).isLinkedWith(apanel)) { - otherJmols.addElement(topJmol); + result.addElement(frame); } } } - return otherJmols; + return result; } void initJmol(String command) @@ -927,6 +933,7 @@ public class AppJmol extends GStructureViewer implements Runnable, worker = null; } + @Override public void pdbFile_actionPerformed(ActionEvent actionEvent) { JalviewFileChooser chooser = new JalviewFileChooser( @@ -964,6 +971,7 @@ public class AppJmol extends GStructureViewer implements Runnable, } } + @Override public void viewMapping_actionPerformed(ActionEvent actionEvent) { jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); @@ -987,23 +995,13 @@ 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.TYPE.EPS); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ + @Override public void png_actionPerformed(ActionEvent e) { makePDBImage(jalview.util.ImageMaker.TYPE.PNG); @@ -1045,15 +1043,17 @@ 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()); @@ -1079,71 +1079,83 @@ 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, @@ -1154,7 +1166,8 @@ public class AppJmol extends GStructureViewer implements Runnable, } } - public void jmolHelp_actionPerformed(ActionEvent actionEvent) + @Override + public void showHelp_actionPerformed(ActionEvent actionEvent) { try { @@ -1274,7 +1287,7 @@ public class AppJmol extends GStructureViewer implements Runnable, this.setTitle(jmb.getViewerTitle()); if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1) { - jmolActionMenu.setVisible(true); + viewerActionMenu.setVisible(true); } if (!jmb.isLoadingFromArchive()) { @@ -1293,11 +1306,11 @@ 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;