X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=3a99f9ece4a9508794b3eebe2c2f6aba8bf449cd;hb=7dc7fb2a35c435d825bc91c5ae60ec6073419a69;hp=e36204cfdb0c4f06ddfb72049690a4135259ca5e;hpb=f976c25c5ad6539698c8fac322362adcc014649d;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index e36204c..3a99f9e 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -110,8 +110,6 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); - protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem(); - protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); @@ -124,8 +122,14 @@ public class PopupMenu extends JPopupMenu JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); + protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem(); + + protected JMenuItem modifyPID = new JMenuItem(); + protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + protected JMenuItem modifyConservation = new JMenuItem(); + AlignmentPanel ap; JMenu sequenceMenu = new JMenu(); @@ -258,7 +262,7 @@ public class PopupMenu extends JPopupMenu { JMenuItem item = new JMenuItem(ff); - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -342,7 +346,7 @@ public class PopupMenu extends JPopupMenu menuItem.setText(MessageManager.formatMessage( "label.2d_rna_structure_line", new Object[] { aa.label })); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -370,7 +374,7 @@ public class PopupMenu extends JPopupMenu menuItem.setText(MessageManager.formatMessage( "label.2d_rna_sequence_name", new Object[] { seq.getName() })); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -391,7 +395,7 @@ public class PopupMenu extends JPopupMenu menuItem = new JMenuItem( MessageManager.getString("action.hide_sequences")); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -407,7 +411,7 @@ public class PopupMenu extends JPopupMenu menuItem = new JMenuItem(MessageManager.formatMessage( "label.represent_group_with", new Object[] { seq.getName() })); - menuItem.addActionListener(new java.awt.event.ActionListener() + menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -538,13 +542,15 @@ public class PopupMenu extends JPopupMenu { if (sg.cs.conservationApplied()) { - conservationMenuItem.setSelected(true); + conservationMenuItem.setSelected(true); } if (sg.cs.getThreshold() > 0) { abovePIDColour.setSelected(true); } } + modifyConservation.setEnabled(conservationMenuItem.isSelected()); + modifyPID.setEnabled(abovePIDColour.isSelected()); displayNonconserved.setSelected(sg.getShowNonconserved()); showText.setSelected(sg.getDisplayText()); showColourText.setSelected(sg.getColourText()); @@ -668,8 +674,6 @@ public class PopupMenu extends JPopupMenu } - - /** * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus. * "All" is added first, followed by a separator. Then add any annotation @@ -785,7 +789,7 @@ public class PopupMenu extends JPopupMenu label = label.substring(1, label.length() - 1); // a, b, c final JMenuItem item = new JMenuItem(label); item.setToolTipText(calcId); - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -967,7 +971,7 @@ public class PopupMenu extends JPopupMenu JMenuItem item = new JMenuItem(label); item.setToolTipText(MessageManager.formatMessage( "label.open_url_param", new Object[] { url })); - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1044,7 +1048,7 @@ public class PopupMenu extends JPopupMenu { groupMenu.setText(MessageManager.getString("label.selection")); groupName.setText(MessageManager.getString("label.name")); - groupName.addActionListener(new java.awt.event.ActionListener() + groupName.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1055,7 +1059,7 @@ public class PopupMenu extends JPopupMenu sequenceMenu.setText(MessageManager.getString("label.sequence")); sequenceName.setText(MessageManager .getString("label.edit_name_description")); - sequenceName.addActionListener(new java.awt.event.ActionListener() + sequenceName.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1065,7 +1069,7 @@ public class PopupMenu extends JPopupMenu }); chooseAnnotations.setText(MessageManager .getString("action.choose_annotations")); - chooseAnnotations.addActionListener(new java.awt.event.ActionListener() + chooseAnnotations.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1075,7 +1079,7 @@ public class PopupMenu extends JPopupMenu }); sequenceDetails.setText(MessageManager .getString("label.sequence_details")); - sequenceDetails.addActionListener(new java.awt.event.ActionListener() + sequenceDetails.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1085,19 +1089,18 @@ public class PopupMenu extends JPopupMenu }); sequenceSelDetails.setText(MessageManager .getString("label.sequence_details")); - sequenceSelDetails - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - sequenceSelectionDetails_actionPerformed(); - } - }); + sequenceSelDetails.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sequenceSelectionDetails_actionPerformed(); + } + }); PIDColour.setFocusPainted(false); unGroupMenuItem .setText(MessageManager.getString("action.remove_group")); - unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + unGroupMenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1107,18 +1110,17 @@ public class PopupMenu extends JPopupMenu }); createGroupMenuItem.setText(MessageManager .getString("action.create_group")); - createGroupMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - createGroupMenuItem_actionPerformed(); - } - }); + createGroupMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + createGroupMenuItem_actionPerformed(); + } + }); outline.setText(MessageManager.getString("action.border_colour")); - outline.addActionListener(new java.awt.event.ActionListener() + outline.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1385,7 +1387,9 @@ public class PopupMenu extends JPopupMenu colourMenu.addSeparator(); colourMenu.add(abovePIDColour); + colourMenu.add(modifyPID); colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); editMenu.add(copy); editMenu.add(cut); editMenu.add(editSequence); @@ -1404,7 +1408,7 @@ public class PopupMenu extends JPopupMenu jMenu1.add(outline); jMenu1.add(displayNonconserved); noColourmenuItem.setText(MessageManager.getString("label.none")); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() + noColourmenuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1415,7 +1419,7 @@ public class PopupMenu extends JPopupMenu clustalColour.setText(MessageManager .getString("label.clustalx_colours")); - clustalColour.addActionListener(new java.awt.event.ActionListener() + clustalColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1424,7 +1428,7 @@ public class PopupMenu extends JPopupMenu } }); zappoColour.setText(MessageManager.getString("label.zappo")); - zappoColour.addActionListener(new java.awt.event.ActionListener() + zappoColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1433,7 +1437,7 @@ public class PopupMenu extends JPopupMenu } }); taylorColour.setText(MessageManager.getString("label.taylor")); - taylorColour.addActionListener(new java.awt.event.ActionListener() + taylorColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1443,17 +1447,16 @@ public class PopupMenu extends JPopupMenu }); hydrophobicityColour.setText(MessageManager .getString("label.hydrophobicity")); - hydrophobicityColour - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(); - } - }); + hydrophobicityColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hydrophobicityColour_actionPerformed(); + } + }); helixColour.setText(MessageManager.getString("label.helix_propensity")); - helixColour.addActionListener(new java.awt.event.ActionListener() + helixColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1463,7 +1466,7 @@ public class PopupMenu extends JPopupMenu }); strandColour.setText(MessageManager .getString("label.strand_propensity")); - strandColour.addActionListener(new java.awt.event.ActionListener() + strandColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1472,7 +1475,7 @@ public class PopupMenu extends JPopupMenu } }); turnColour.setText(MessageManager.getString("label.turn_propensity")); - turnColour.addActionListener(new java.awt.event.ActionListener() + turnColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1481,7 +1484,7 @@ public class PopupMenu extends JPopupMenu } }); buriedColour.setText(MessageManager.getString("label.buried_index")); - buriedColour.addActionListener(new java.awt.event.ActionListener() + buriedColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1489,19 +1492,9 @@ public class PopupMenu extends JPopupMenu buriedColour_actionPerformed(); } }); - abovePIDColour.setText(MessageManager - .getString("label.above_identity_percentage")); - abovePIDColour.addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - abovePIDColour_actionPerformed(); - } - }); userDefinedColour.setText(MessageManager .getString("action.user_defined")); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() + userDefinedColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1511,7 +1504,7 @@ public class PopupMenu extends JPopupMenu }); PIDColour .setText(MessageManager.getString("label.percentage_identity")); - PIDColour.addActionListener(new java.awt.event.ActionListener() + PIDColour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1520,7 +1513,7 @@ public class PopupMenu extends JPopupMenu } }); BLOSUM62Colour.setText(MessageManager.getString("label.blosum62")); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() + BLOSUM62Colour.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) @@ -1530,33 +1523,87 @@ public class PopupMenu extends JPopupMenu }); purinePyrimidineColour.setText(MessageManager .getString("label.purine_pyrimidine")); - purinePyrimidineColour - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - purinePyrimidineColour_actionPerformed(); - } - }); + purinePyrimidineColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + purinePyrimidineColour_actionPerformed(); + } + }); /* - * covariationColour.addActionListener(new java.awt.event.ActionListener() { + * covariationColour.addActionListener(new ActionListener() { * public void actionPerformed(ActionEvent e) { * covariationColour_actionPerformed(); } }); */ + abovePIDColour.setText(MessageManager + .getString("label.above_identity_percentage")); + abovePIDColour.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + abovePIDColour_actionPerformed(); + } + }); + + modifyPID.setText(MessageManager + .getString("label.modify_identity_threshold")); + modifyPID.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + modifyPID_actionPerformed(); + } + }); conservationMenuItem.setText(MessageManager .getString("label.conservation")); - conservationMenuItem - .addActionListener(new java.awt.event.ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - conservationMenuItem_actionPerformed(); - } - }); + conservationMenuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + conservationMenuItem_actionPerformed(); + } + }); + + modifyConservation.setText(MessageManager + .getString("label.modify_conservation_threshold")); + modifyConservation.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + modifyConservation_actionPerformed(); + } + }); + } + + protected void modifyConservation_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs != null) + { + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.showConservationSlider(); + } + } + + protected void modifyPID_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs != null) + { + // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() + // .getName()); + // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus()); + SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() + .getName()); + SliderPanel.showPIDSlider(); + } } /** @@ -1863,7 +1910,8 @@ public class PopupMenu extends JPopupMenu return; } - if (abovePIDColour.isSelected()) + boolean selected = abovePIDColour.isSelected(); + if (selected) { sg.cs.setConsensus(AAFrequency.calculate( sg.getSequences(ap.av.getHiddenRepSequences()), @@ -1880,7 +1928,9 @@ public class PopupMenu extends JPopupMenu // remove PIDColouring { sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); + SliderPanel.hidePIDSlider(); } + modifyPID.setEnabled(selected); refresh(); } @@ -1982,7 +2032,8 @@ public class PopupMenu extends JPopupMenu return; } - if (conservationMenuItem.isSelected()) + boolean selected = conservationMenuItem.isSelected(); + if (selected) { // JBPNote: Conservation name shouldn't be i18n translated Conservation c = new Conservation("Group", sg.getSequences(ap.av @@ -2001,7 +2052,9 @@ public class PopupMenu extends JPopupMenu // remove ConservationColouring { sg.cs.setConservation(null); + SliderPanel.hideConservationSlider(); } + modifyConservation.setEnabled(selected); refresh(); }