X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=41a4bf7eea6040356efb12df8d873ce358e3c1bb;hb=ec669c13867d001e07c9cef157c268afe03be9f3;hp=998db4b14c3eb035551eba9cc8f9071b56abd0f1;hpb=aced09c4feeaf3406269442c14e54abeeb4cad81;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 998db4b..41a4bf7 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. @@ -20,28 +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.api.structures.JalviewStructureDisplayI; 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.datamodel.SequenceI; import jalview.ext.jmol.JalviewJmolBinding; -import jalview.io.*; -import jalview.schemes.*; +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; +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.ArrayList; +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, ViewSetProvider, JalviewStructureDisplayI @@ -70,6 +106,7 @@ 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) { @@ -79,6 +116,7 @@ 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) @@ -138,14 +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(); @@ -167,7 +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(); @@ -213,8 +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 @@ -265,8 +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. @@ -328,7 +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); @@ -495,7 +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) @@ -576,25 +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) @@ -643,7 +687,9 @@ 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; @@ -660,7 +706,9 @@ public class AppJmol extends GStructureViewer implements Runnable, public void itemStateChanged(ItemEvent evt) { if (!allChainsSelected) + { centerViewer(); + } } }); @@ -885,6 +933,7 @@ public class AppJmol extends GStructureViewer implements Runnable, worker = null; } + @Override public void pdbFile_actionPerformed(ActionEvent actionEvent) { JalviewFileChooser chooser = new JalviewFileChooser( @@ -922,6 +971,7 @@ public class AppJmol extends GStructureViewer implements Runnable, } } + @Override public void viewMapping_actionPerformed(ActionEvent actionEvent) { jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); @@ -945,46 +995,45 @@ 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) { @@ -994,15 +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()); @@ -1028,71 +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, @@ -1103,7 +1166,8 @@ public class AppJmol extends GStructureViewer implements Runnable, } } - public void jmolHelp_actionPerformed(ActionEvent actionEvent) + @Override + public void showHelp_actionPerformed(ActionEvent actionEvent) { try { @@ -1223,7 +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()) { @@ -1242,11 +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;