X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=0861f2d4250d8fdc07ac7fc623e582aa4dd59596;hb=c86442e455c858f4a092fbb2e9394faa3e161a89;hp=4f7e2b98c682973a543c26feba66af5557857d90;hpb=2e2e6d269fbaa505151fe777374f41111f2910d5;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 4f7e2b9..0861f2d 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -20,46 +20,13 @@ */ package jalview.appletgui; -import java.awt.BorderLayout; -import java.awt.Canvas; -import java.awt.CheckboxMenuItem; -import java.awt.Color; -import java.awt.Font; -import java.awt.FontMetrics; -import java.awt.Frame; -import java.awt.Graphics; -import java.awt.Label; -import java.awt.Menu; -import java.awt.MenuBar; -import java.awt.MenuItem; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.FocusEvent; -import java.awt.event.FocusListener; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.awt.event.KeyEvent; -import java.awt.event.KeyListener; -import java.awt.event.WindowAdapter; -import java.awt.event.WindowEvent; -import java.io.IOException; -import java.net.URL; -import java.net.URLEncoder; -import java.util.Arrays; -import java.util.Deque; -import java.util.HashMap; -import java.util.Hashtable; -import java.util.List; -import java.util.Map; -import java.util.StringTokenizer; -import java.util.Vector; - import jalview.analysis.AlignmentSorter; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.api.AlignViewControllerGuiI; import jalview.api.AlignViewControllerI; import jalview.api.AlignViewportI; import jalview.api.FeatureRenderer; +import jalview.api.FeatureSettingsControllerI; import jalview.api.SequenceStructureBinding; import jalview.bin.JalviewLite; import jalview.commands.CommandI; @@ -93,7 +60,6 @@ import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; import jalview.schemes.RNAHelicesColourChooser; -import jalview.schemes.RNAInteractionColourScheme; import jalview.schemes.StrandColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.schemes.TaylorColourScheme; @@ -105,6 +71,42 @@ import jalview.util.MappingUtils; import jalview.util.MessageManager; import jalview.viewmodel.AlignmentViewport; +import java.awt.BorderLayout; +import java.awt.Canvas; +import java.awt.CheckboxMenuItem; +import java.awt.Color; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Frame; +import java.awt.Graphics; +import java.awt.Label; +import java.awt.Menu; +import java.awt.MenuBar; +import java.awt.MenuItem; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.FocusEvent; +import java.awt.event.FocusListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyEvent; +import java.awt.event.KeyListener; +import java.awt.event.WindowAdapter; +import java.awt.event.WindowEvent; +import java.io.IOException; +import java.net.URL; +import java.net.URLEncoder; +import java.util.Arrays; +import java.util.Deque; +import java.util.HashMap; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; +import java.util.StringTokenizer; +import java.util.Vector; + +import org.jmol.viewer.Viewer; + public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener, AlignViewControllerGuiI { @@ -209,7 +211,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, if (hiddenSeqs != null && hiddenSeqs.length > 0) { viewport.hideSequence(hiddenSeqs); - viewport.setHasHiddenRows(true); } if (columnSelection != null) { @@ -927,7 +928,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, : showForSequences); aa.visible = visible; } - alignPanel.validateAnnotationDimensions(false); + alignPanel.validateAnnotationDimensions(true); + validate(); + repaint(); } private void setAnnotationSortOrder(SequenceAnnotationOrder order) @@ -1226,10 +1229,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { changeColour(new PurinePyrimidineColourScheme()); } - else if (source == RNAInteractionColour) - { - changeColour(new RNAInteractionColourScheme()); - } + // else if (source == RNAInteractionColour) + // { + // changeColour(new RNAInteractionColourScheme()); + // } else if (source == RNAHelixColour) { new RNAHelicesColourChooser(viewport, alignPanel); @@ -1340,8 +1343,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { e.getActionCommand() }), 600, 500); FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer(); - viewport.setFeatureRenderer(fr); - cap.setText(new AppletFormatAdapter(viewport).formatSequences( + cap.setText(new AppletFormatAdapter(alignPanel).formatSequences( e.getActionCommand(), viewport.getAlignment(), viewport.getShowJVSuffix())); } @@ -2572,7 +2574,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public void changeColour(ColourSchemeI cs) { - int threshold = 0; if (cs != null) { @@ -2595,15 +2596,6 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, } viewport.setGlobalColourScheme(cs); - if (alignPanel.getOverviewPanel() != null) - { - alignPanel.getOverviewPanel().updateOverviewImage(); - } - - jalview.structure.StructureSelectionManager - .getStructureSelectionManager(viewport.applet) - .sequenceColoursChanged(alignPanel); - alignPanel.paintAlignment(true); } @@ -2999,10 +2991,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MessageManager.getString("label.load_features_annotations")); MenuItem outputFeatures = new MenuItem( - MessageManager.getString("label.export_features").concat("...")); + MessageManager.getString("label.export_features")); MenuItem outputAnnotations = new MenuItem( - MessageManager.getString("label.export_annotations").concat("...")); + MessageManager.getString("label.export_annotations")); MenuItem closeMenuItem = new MenuItem( MessageManager.getString("action.close")); @@ -3068,7 +3060,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, MenuItem purinePyrimidineColour = new MenuItem(); - MenuItem RNAInteractionColour = new MenuItem(); + // MenuItem RNAInteractionColour = new MenuItem(); MenuItem RNAHelixColour = new MenuItem(); @@ -3251,8 +3243,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, removeAllGapsMenuItem.setLabel(MessageManager .getString("action.remove_all_gaps")); removeAllGapsMenuItem.addActionListener(this); - removeRedundancyMenuItem.setLabel(MessageManager.getString( - "action.remove_redundancy").concat("...")); + removeRedundancyMenuItem.setLabel(MessageManager + .getString("action.remove_redundancy")); removeRedundancyMenuItem.addActionListener(this); /* @@ -3276,7 +3268,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, grpsFromSelection.addActionListener(this); createGroup.setLabel(MessageManager.getString("action.create_group")); unGroup.setLabel(MessageManager.getString("action.remove_group")); - annotationColumnSelection.setLabel("Select by Annotation"); + annotationColumnSelection.setLabel(MessageManager + .getString("action.select_by_annotation")); annotationColumnSelection.addActionListener(this); /* @@ -3306,7 +3299,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, hideAllSelection.addActionListener(this); showAllHidden.addActionListener(this); featureSettings.setLabel(MessageManager - .getString("label.feature_settings")); + .getString("action.feature_settings")); featureSettings.addActionListener(this); sequenceFeatures.setLabel(MessageManager .getString("label.show_sequence_features")); @@ -3438,9 +3431,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, purinePyrimidineColour.setLabel(MessageManager .getString("label.purine_pyrimidine")); purinePyrimidineColour.addActionListener(this); - RNAInteractionColour.setLabel(MessageManager - .getString("label.rna_interaction")); - RNAInteractionColour.addActionListener(this); + // RNAInteractionColour.setLabel(MessageManager + // .getString("label.rna_interaction")); + // RNAInteractionColour.addActionListener(this); RNAHelixColour.setLabel(MessageManager .getString("action.by_rna_helixes")); RNAHelixColour.addActionListener(this); @@ -3871,10 +3864,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, public SequenceStructureBinding addStructureViewInstance( Object jmolviewer, String[] sequenceIds) { - org.jmol.api.JmolViewer viewer = null; + Viewer viewer = null; try { - viewer = (org.jmol.api.JmolViewer) jmolviewer; + viewer = (Viewer) jmolviewer; } catch (ClassCastException ex) { System.err.println("Unsupported viewer object :" @@ -3947,7 +3940,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, boolean needtoadd = false; if (toaddpdb != null) { - Vector pdbe = toaddpdb.getPDBId(); + Vector pdbe = toaddpdb.getAllPDBEntries(); PDBEntry pdbentry = null; if (pdbe != null && pdbe.size() > 0) { @@ -4206,4 +4199,36 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, { this.splitFrame = sf; } + + // may not need this + @Override + public void setShowSeqFeatures(boolean b) + { + // showSeqFeatures.setSelected(b); + viewport.setShowSequenceFeatures(b); + + } + + @Override + public void setMenusForViewport() + { + // setMenusFromViewport(viewport); + + } + @Override + public void refreshFeatureUI(boolean enableIfNecessary) + { + if (enableIfNecessary) + { + sequenceFeatures.setState(true); + alignPanel.av.setShowSequenceFeatures(true); + } + } + + @Override + public FeatureSettingsControllerI getFeatureSettingsUI() + { + return alignPanel.av.featureSettings; + } + }