X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=cfd3d00d66a5b67a7db59bc14fcc6b86622cf84a;hb=06ce849ffedc7ab10a3c54cda96b9a7dec58c136;hp=14b3e6abab8b9e18e1bf3b5e954f845ab29e8582;hpb=b5699e7d9cc2045f623609948ee10a736256abc4;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 14b3e6a..cfd3d00 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -52,6 +52,8 @@ import jalview.io.AppletFormatAdapter; import jalview.io.DataSourceType; import jalview.io.FeaturesFile; import jalview.io.FileFormat; +import jalview.io.FileFormatI; +import jalview.io.FileFormats; import jalview.io.TCoffeeScoreFile; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; @@ -62,6 +64,7 @@ import jalview.schemes.HydrophobicColourScheme; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; +import jalview.schemes.RNAHelicesColour; import jalview.schemes.RNAHelicesColourChooser; import jalview.schemes.StrandColourScheme; import jalview.schemes.TCoffeeColourScheme; @@ -1256,7 +1259,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, // } else if (source == RNAHelixColour) { - new RNAHelicesColourChooser(viewport, alignPanel); + changeColour(new RNAHelicesColour(viewport.getAlignment())); + // new RNAHelicesColourChooser(viewport, alignPanel); } else if (source == modifyPID) { @@ -1363,7 +1367,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, "label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); - FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand()); + FileFormatI fileFormat = FileFormats.getInstance().forName( + e.getActionCommand()); cap.setText(new AppletFormatAdapter(alignPanel).formatSequences( fileFormat, viewport.getAlignment(), viewport.getShowJVSuffix())); @@ -1481,10 +1486,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, url.append(appendProtocol(viewport.applet.getParameter("annotations"))); } - if (viewport.applet.getParameter("jnetfile") != null) + if (viewport.applet.getParameter("jnetfile") != null + || viewport.applet.getParameter("jpredfile") != null) { url.append("&annotations="); - url.append(appendProtocol(viewport.applet.getParameter("jnetfile"))); + url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet + .getParameter("jnetfile") : viewport.applet + .getParameter("jpredfile"))); } if (viewport.applet.getParameter("defaultColour") != null) @@ -2673,26 +2681,43 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, protected void conservationMenuItem_actionPerformed() { - viewport.setConservationSelected(conservationMenuItem.getState()); + boolean selected = conservationMenuItem.getState(); + modifyConservation.setEnabled(selected); + viewport.setConservationSelected(selected); - viewport.setAbovePIDThreshold(false); - abovePIDThreshold.setState(false); + // viewport.setAbovePIDThreshold(false); + // abovePIDThreshold.setState(false); changeColour(viewport.getGlobalColourScheme()); - modifyConservation_actionPerformed(); + if (selected) + { + modifyConservation_actionPerformed(); + } + else + { + SliderPanel.hideConservationSlider(); + } } public void abovePIDThreshold_actionPerformed() { - viewport.setAbovePIDThreshold(abovePIDThreshold.getState()); - - conservationMenuItem.setState(false); - viewport.setConservationSelected(false); + boolean selected = abovePIDThreshold.getState(); + modifyPID.setEnabled(selected); + viewport.setAbovePIDThreshold(selected); + // conservationMenuItem.setState(false); + // viewport.setConservationSelected(false); changeColour(viewport.getGlobalColourScheme()); - modifyPID_actionPerformed(); + if (selected) + { + modifyPID_actionPerformed(); + } + else + { + SliderPanel.hidePIDSlider(); + } } public void sortPairwiseMenuItem_actionPerformed() @@ -3237,7 +3262,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, inputText.addActionListener(this); Menu outputTextboxMenu = new Menu( MessageManager.getString("label.out_to_textbox")); - for (String ff : FileFormat.getWritableFormats(true)) + for (String ff : FileFormats.getInstance().getWritableFormats(true)) { MenuItem item = new MenuItem(ff); @@ -3460,45 +3485,50 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getString("label.apply_colour_to_all_groups")); applyToAllGroups.setState(true); applyToAllGroups.addItemListener(this); - clustalColour.setLabel(MessageManager.getString("label.clustalx")); + clustalColour.setLabel(MessageManager + .getString("label.colourScheme_clustal")); clustalColour.addActionListener(this); - zappoColour.setLabel(MessageManager.getString("label.zappo")); + zappoColour.setLabel(MessageManager + .getString("label.colourScheme_zappo")); zappoColour.addActionListener(this); - taylorColour.setLabel(MessageManager.getString("label.taylor")); + taylorColour.setLabel(MessageManager + .getString("label.colourScheme_taylor")); taylorColour.addActionListener(this); hydrophobicityColour.setLabel(MessageManager - .getString("label.hydrophobicity")); + .getString("label.colourScheme_hydrophobic")); hydrophobicityColour.addActionListener(this); - helixColour - .setLabel(MessageManager.getString("label.helix_propensity")); + helixColour.setLabel(MessageManager + .getString("label.colourScheme_helix_propensity")); helixColour.addActionListener(this); strandColour.setLabel(MessageManager - .getString("label.strand_propensity")); + .getString("label.colourScheme_strand_propensity")); strandColour.addActionListener(this); - turnColour.setLabel(MessageManager.getString("label.turn_propensity")); + turnColour.setLabel(MessageManager + .getString("label.colourScheme_turn_propensity")); turnColour.addActionListener(this); - buriedColour.setLabel(MessageManager.getString("label.buried_index")); + buriedColour.setLabel(MessageManager + .getString("label.colourScheme_buried_index")); buriedColour.addActionListener(this); purinePyrimidineColour.setLabel(MessageManager - .getString("label.purine_pyrimidine")); + .getString("label.colourScheme_purine/pyrimidine")); purinePyrimidineColour.addActionListener(this); // RNAInteractionColour.setLabel(MessageManager // .getString("label.rna_interaction")); // RNAInteractionColour.addActionListener(this); RNAHelixColour.setLabel(MessageManager - .getString("action.by_rna_helixes")); + .getString("label.colourScheme_rna_helices")); RNAHelixColour.addActionListener(this); userDefinedColour.setLabel(MessageManager .getString("action.user_defined")); userDefinedColour.addActionListener(this); PIDColour.setLabel(MessageManager - .getString("label.percentage_identity")); + .getString("label.colourScheme_%_identity")); PIDColour.addActionListener(this); BLOSUM62Colour.setLabel(MessageManager - .getString("label.blosum62_score")); + .getString("label.colourScheme_blosum62")); BLOSUM62Colour.addActionListener(this); - tcoffeeColour - .setLabel(MessageManager.getString("label.tcoffee_scores")); + tcoffeeColour.setLabel(MessageManager + .getString("label.colourScheme_t-coffee_scores")); // it will be enabled only if a score file is provided tcoffeeColour.setEnabled(false); tcoffeeColour.addActionListener(this); @@ -3510,13 +3540,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, abovePIDThreshold.setLabel(MessageManager .getString("label.above_identity_threshold")); abovePIDThreshold.addItemListener(this); - nucleotideColour.setLabel(MessageManager.getString("label.nucleotide")); + nucleotideColour.setLabel(MessageManager + .getString("label.colourScheme_nucleotide")); nucleotideColour.addActionListener(this); modifyPID.setLabel(MessageManager .getString("label.modify_identity_threshold")); + modifyPID.setEnabled(abovePIDThreshold.getState()); modifyPID.addActionListener(this); modifyConservation.setLabel(MessageManager .getString("label.modify_conservation_threshold")); + modifyConservation.setEnabled(conservationMenuItem.getState()); modifyConservation.addActionListener(this); annotationColour.setLabel(MessageManager .getString("action.by_annotation")); @@ -3550,7 +3583,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, .getString("label.neighbour_joining_identity")); neighbourTreeMenuItem.addActionListener(this); avDistanceTreeBlosumMenuItem.setLabel(MessageManager - .getString("label.average_distance_bloslum62")); + .getString("label.average_distance_blosum62")); avDistanceTreeBlosumMenuItem.addActionListener(this); njTreeBlosumMenuItem.setLabel(MessageManager .getString("label.neighbour_blosum62"));