X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;fp=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=1fd4231ee4d203a885fc7fd827a571ed20f23fe8;hb=a4677746324adeea9632d7306c83dfd94dff6181;hp=0225dc7554b17eae3684b49fe36ad0d62f797587;hpb=7d6575e94bed92bc06043d432576e3a39e8a8e75;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 0225dc7..1fd4231 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -37,6 +37,7 @@ import jalview.commands.RemoveGapColCommand; import jalview.commands.RemoveGapsCommand; import jalview.commands.SlideSequencesCommand; import jalview.commands.TrimRegionCommand; +import jalview.controller.AlignViewController; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; @@ -46,9 +47,11 @@ import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; import jalview.io.AppletFormatAdapter; import jalview.io.FeaturesFile; +import jalview.io.NewickFile; import jalview.io.TCoffeeScoreFile; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; @@ -68,6 +71,7 @@ import jalview.schemes.TurnColourScheme; import jalview.schemes.ZappoColourScheme; import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; +import jalview.util.Comparison; import jalview.util.MappingUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; @@ -219,7 +223,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } alignPanel = new AlignmentPanel(this, viewport); - avc = new jalview.controller.AlignViewController(this, viewport, + avc = new AlignViewController(this, viewport, alignPanel); viewport.updateConservation(alignPanel); viewport.updateConsensus(alignPanel); @@ -366,7 +370,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, boolean featuresFile = false; try { - featuresFile = new jalview.io.FeaturesFile(file, type) + featuresFile = new FeaturesFile(file, type) .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas .getFeatureRenderer().getFeatureColours(), featureLinks, true, viewport.applet.getDefaultParameter( @@ -1171,13 +1175,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } else if (source == alProperties) { - StringBuffer contents = new jalview.io.AlignmentProperties( + StringBuffer contents = new AlignmentProperties( viewport.getAlignment()).formatAsString(); CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); cap.setText(contents.toString()); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + JalviewLite.addFrame(frame, MessageManager.formatMessage( "label.alignment_properties", new String[] { getTitle() }), 400, 250); } @@ -1330,7 +1334,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, + JalviewLite.addFrame(frame, MessageManager.getString("label.input_cut_paste"), 500, 500); } @@ -1339,7 +1343,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + JalviewLite.addFrame(frame, MessageManager.formatMessage( "label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); @@ -1357,7 +1361,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, cap.setAnnotationImport(); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, + JalviewLite.addFrame(frame, MessageManager.getString("action.paste_annotations"), 400, 300); } @@ -1372,7 +1376,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, + JalviewLite.addFrame(frame, MessageManager.getString("label.annotations"), 600, 500); cap.setText(annotation); } @@ -1422,7 +1426,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, + JalviewLite.addFrame(frame, MessageManager.getString("label.features"), 600, 500); cap.setText(features); } @@ -1918,7 +1922,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++) { ch = seq.getCharAt(j); - if (!jalview.util.Comparison.isGap((ch))) + if (!Comparison.isGap((ch))) { endRes++; } @@ -1998,7 +2002,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } } - jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth, + JalviewLite.addFrame(af, newtitle, frameWidth, frameHeight); } else @@ -2550,7 +2554,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, OverviewPanel overview = new OverviewPanel(alignPanel); frame.add(overview); // +50 must allow for applet frame window - jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( + JalviewLite.addFrame(frame, MessageManager.formatMessage( "label.overview_params", new String[] { this.getTitle() }), overview.getPreferredSize().width, overview.getPreferredSize().height + 50); @@ -2603,8 +2607,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, alignPanel.getOverviewPanel().updateOverviewImage(); } - jalview.structure.StructureSelectionManager - .getStructureSelectionManager(viewport.applet) + StructureSelectionManager.getStructureSelectionManager(viewport.applet) .sequenceColoursChanged(alignPanel); alignPanel.paintAlignment(true); @@ -2707,7 +2710,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { Frame frame = new Frame(); frame.add(new PairwiseAlignPanel(alignPanel)); - jalview.bin.JalviewLite.addFrame(frame, + JalviewLite.addFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600, 500); } @@ -2799,7 +2802,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, addTreeMenuItem(tp, title); - jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); + JalviewLite.addFrame(tp, title, 600, 500); } } @@ -2810,15 +2813,15 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, cap.setTreeImport(); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, + JalviewLite.addFrame(frame, MessageManager.getString("label.paste_newick_file"), 400, 300); } - public void loadTree(jalview.io.NewickFile tree, String treeFile) + public void loadTree(NewickFile tree, String treeFile) { TreePanel tp = new TreePanel(alignPanel, treeFile, MessageManager.getString("label.load_tree_from_file"), tree); - jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); + JalviewLite.addFrame(tp, treeFile, 600, 500); addTreeMenuItem(tp, treeFile); } @@ -2968,7 +2971,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, Frame frame = new Frame(); frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite .getBuildDate())); - jalview.bin.JalviewLite.addFrame(frame, + JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220); } @@ -3198,11 +3201,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, inputText.addActionListener(this); Menu outputTextboxMenu = new Menu( MessageManager.getString("label.out_to_textbox")); - for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) + for (int i = 0; i < AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) { - MenuItem item = new MenuItem( - jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); + MenuItem item = new MenuItem(AppletFormatAdapter.WRITEABLE_FORMATS[i]); item.addActionListener(new java.awt.event.ActionListener() { @@ -3806,7 +3808,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, add(statusBar, BorderLayout.SOUTH); add(alignPanel, BorderLayout.CENTER); // and register with the applet so it can pass external API calls to us - jalview.bin.JalviewLite.addFrame(this, this.getTitle(), + JalviewLite.addFrame(this, this.getTitle(), frameWidth, frameHeight); } @@ -4064,12 +4066,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { // can only do alignments with Jmol // find the last jmol window assigned to this alignment - jalview.appletgui.AppletJmol ajm = null, tajm; + AppletJmol ajm = null, tajm; Vector jmols = applet - .getAppletWindow(jalview.appletgui.AppletJmol.class); +.getAppletWindow(AppletJmol.class); for (int i = 0, iSize = jmols.size(); i < iSize; i++) { - tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i); + tajm = (AppletJmol) jmols.elementAt(i); if (tajm.ap.alignFrame == this) { ajm = tajm; @@ -4088,8 +4090,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // otherwise, create a new window if (applet.jmolAvailable) { - new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel, - protocol); + new AppletJmol(pdb, seqs, chains, alignPanel, protocol); applet.lastFrameX += 40; applet.lastFrameY += 40; }