X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=3401cc4b31d676978eb35fa75ec243603051d7ee;hb=2ac5b6423fe366e093c8f12b0935aefc9aafbe5f;hp=42643d0877e4c5ce52f16c0c5d5195b218680711;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 42643d0..3401cc4 100755 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -1,31 +1,34 @@ /* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle -* -* This program is free software; you can redistribute it and/or -* modify it under the terms of the GNU General Public License -* as published by the Free Software Foundation; either version 2 -* of the License, or (at your option) any later version. -* -* This program is distributed in the hope that it will be useful, -* but WITHOUT ANY WARRANTY; without even the implied warranty of -* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -* GNU General Public License for more details. -* -* You should have received a copy of the GNU General Public License -* along with this program; if not, write to the Free Software -* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA -*/ + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.appletgui; -import jalview.datamodel.*; -import jalview.analysis.*; -import jalview.schemes.*; import java.awt.*; import java.awt.event.*; +import java.util.Vector; + +import jalview.analysis.*; +import jalview.datamodel.*; +import jalview.schemes.*; -public class APopupMenu extends java.awt.PopupMenu +public class APopupMenu + extends java.awt.PopupMenu implements ActionListener, ItemListener { Menu groupMenu = new Menu(); protected MenuItem clustalColour = new MenuItem(); @@ -43,19 +46,21 @@ public class APopupMenu extends java.awt.PopupMenu MenuItem noColourmenuItem = new MenuItem(); protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); - - AlignmentPanel ap; - Menu sequenceMenu = new Menu(); - MenuItem sequenceName = new MenuItem(); - Sequence sequence; + final AlignmentPanel ap; MenuItem unGroupMenuItem = new MenuItem(); MenuItem nucleotideMenuItem = new MenuItem(); Menu colourMenu = new Menu(); CheckboxMenuItem showBoxes = new CheckboxMenuItem(); CheckboxMenuItem showText = new CheckboxMenuItem(); CheckboxMenuItem showColourText = new CheckboxMenuItem(); - - public APopupMenu(AlignmentPanel ap, Sequence seq) + Menu editMenu = new Menu("Edit"); + MenuItem copy = new MenuItem("Copy (Jalview Only)"); + MenuItem cut = new MenuItem("Cut (Jalview Only)"); + MenuItem toUpper = new MenuItem("To Upper Case"); + MenuItem toLower = new MenuItem("To Lower Case"); + MenuItem toggleCase = new MenuItem("Toggle Case"); + + public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links) { /////////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -64,107 +69,202 @@ public class APopupMenu extends java.awt.PopupMenu // If from the IDPanel, we must display the sequence menu ////////////////////////////////////////////////////////// - this.ap = ap; - sequence = seq; + this.ap = apanel; try - { jbInit(); } - catch(Exception e) - { e.printStackTrace(); } - + { + jbInit(); + } + catch (Exception e) + { + e.printStackTrace(); + } SequenceGroup sg = ap.av.getSelectionGroup(); - if(sg!=null) + + if (sg != null && sg.getSize(false)>0) { showText.setState(sg.getDisplayText()); showColourText.setState(sg.getColourText()); showBoxes.setState(sg.getDisplayBoxes()); - } - - if( !ap.av.alignment.getGroups().contains(sg)) + if (!ap.av.alignment.getGroups().contains(sg)) + { groupMenu.remove(unGroupMenuItem); + } - if(seq==null) - remove(sequenceMenu); + } + else + { + remove(groupMenu); + remove(editMenu); + } + if (links!=null) + { + Menu linkMenu = new Menu("Link"); + MenuItem item; + String link; + for(int i=0; i -1) + { + String id = seq.getName(); + if (id.indexOf("|") > -1) + id = id.substring(id.lastIndexOf("|") + 1); + + url = link.substring(link.indexOf("|") + 1, + link.indexOf("$SEQUENCE_ID$")) + + id + + link.substring(link.indexOf("$SEQUENCE_ID$") + 13); + } + else + url = link.substring(link.lastIndexOf("|")+1); + + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + ap.alignFrame.showURL(url, target); + } + }); + linkMenu.add(item); + } + add(linkMenu); + if(seq!=null) + { + item = new MenuItem("Show PDB Structure"); + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + addPDB(seq); + } + }); + + add(item); + } + } } - private void jbInit() throws Exception + + public void itemStateChanged(ItemEvent evt) { - groupMenu.setLabel("Group"); - groupMenu.setLabel("Define"); + if(evt.getSource()==abovePIDColour) + abovePIDColour_itemStateChanged(); + else if(evt.getSource()==showColourText) + showColourText_itemStateChanged(); + else if(evt.getSource()==showText) + showText_itemStateChanged(); + else if(evt.getSource()==showBoxes) + showBoxes_itemStateChanged() ; + } - sequenceMenu.setLabel("Sequence"); - sequenceName.setLabel("Edit name"); - unGroupMenuItem.setLabel("Remove Group"); - unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + public void actionPerformed(ActionEvent evt) + { + Object source = evt.getSource(); + if(source==clustalColour) + clustalColour_actionPerformed(); + else if(source==zappoColour) + zappoColour_actionPerformed(); + else if(source==taylorColour) + taylorColour_actionPerformed(); + else if(source==hydrophobicityColour) + hydrophobicityColour_actionPerformed(); + else if(source==helixColour) + helixColour_actionPerformed(); + else if(source==strandColour) + strandColour_actionPerformed(); + else if(source==clustalColour) + turnColour_actionPerformed(); + else if(source==buriedColour) + buriedColour_actionPerformed(); + else if(source==nucleotideMenuItem) + nucleotideMenuItem_actionPerformed(); + + else if(source==userDefinedColour) + userDefinedColour_actionPerformed(); + else if(source==PIDColour) + PIDColour_actionPerformed(); + else if(source==BLOSUM62Colour) + BLOSUM62Colour_actionPerformed(); + else if(source==noColourmenuItem) + noColourmenuItem_actionPerformed(); + else if(source==conservationMenuItem) + conservationMenuItem_itemStateChanged(); + else if(source==unGroupMenuItem) + unGroupMenuItem_actionPerformed(); + + else if(source==copy) + ap.alignFrame.copy_actionPerformed(); + else if(source==cut) + ap.alignFrame.cut_actionPerformed(); + else if(source==toUpper || source==toLower || source==toggleCase) { - public void actionPerformed(ActionEvent e) + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg != null) { - unGroupMenuItem_actionPerformed(e); + for (int g = 0; g < sg.getSize(true); g++) + { + if (source == toggleCase) + ((SequenceI) sg.getSequences(true).elementAt(g)) + .toggleCase(sg.getStartRes(), sg.getEndRes() + 1); + else + ((SequenceI) sg.getSequences(true).elementAt(g)) + .changeCase(source == toUpper, sg.getStartRes(), + sg.getEndRes() + 1); + } + ap.seqPanel.seqCanvas.repaint(); } - }); + } + + } + void addPDB(Sequence seq) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame); + cap.setText("Paste your PDB file here."); + cap.setPDBImport(seq); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300); + } + + private void jbInit() + throws Exception + { + groupMenu.setLabel("Group"); + groupMenu.setLabel("Define"); + + unGroupMenuItem.setLabel("Remove Group"); + unGroupMenuItem.addActionListener(this); nucleotideMenuItem.setLabel("Nucleotide"); - nucleotideMenuItem.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - nucleotideMenuItem_actionPerformed(e); - } - }); - conservationMenuItem.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent itemEvent) - { - conservationMenuItem_itemStateChanged(itemEvent); - } - }); - abovePIDColour.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent itemEvent) - { - abovePIDColour_itemStateChanged(itemEvent); - } - }); + nucleotideMenuItem.addActionListener(this); + conservationMenuItem.addItemListener(this); + abovePIDColour.addItemListener(this); colourMenu.setLabel("Group Colour"); showBoxes.setLabel("Boxes"); showBoxes.setState(true); - showBoxes.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent itemEvent) - { - showBoxes_itemStateChanged(itemEvent); - } - }); + showBoxes.addItemListener(this); showText.setLabel("Text"); - showText.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent itemEvent) - { - showText_itemStateChanged(itemEvent); - } - }); + showText.addItemListener(this); showColourText.setLabel("Colour Text"); - showColourText.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent itemEvent) - { - showColourText_itemStateChanged(itemEvent); - } - }); + showColourText.addItemListener(this); add(groupMenu); - this.add(sequenceMenu); groupMenu.add(unGroupMenuItem); groupMenu.add(colourMenu); groupMenu.addSeparator(); groupMenu.add(showBoxes); groupMenu.add(showText); groupMenu.add(showColourText); - sequenceMenu.add(sequenceName); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); colourMenu.add(BLOSUM62Colour); @@ -183,324 +283,232 @@ public class APopupMenu extends java.awt.PopupMenu colourMenu.add(conservationMenuItem); noColourmenuItem.setLabel("None"); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - noColourmenuItem_actionPerformed(e); - } - }); + noColourmenuItem.addActionListener(this); clustalColour.setLabel("Clustalx colours"); - clustalColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - clustalColour_actionPerformed(e); - } - }); + clustalColour.addActionListener(this); zappoColour.setLabel("Zappo"); - zappoColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - zappoColour_actionPerformed(e); - } - }); + zappoColour.addActionListener(this); taylorColour.setLabel("Taylor"); - taylorColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - taylorColour_actionPerformed(e); - } - }); + taylorColour.addActionListener(this); hydrophobicityColour.setLabel("Hydrophobicity"); - hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(e); - } - }); + hydrophobicityColour.addActionListener(this); helixColour.setLabel("Helix propensity"); - helixColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - helixColour_actionPerformed(e); - } - }); + helixColour.addActionListener(this); strandColour.setLabel("Strand propensity"); - strandColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - strandColour_actionPerformed(e); - } - }); + strandColour.addActionListener(this); turnColour.setLabel("Turn propensity"); - turnColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - turnColour_actionPerformed(e); - } - }); + turnColour.addActionListener(this); buriedColour.setLabel("Buried Index"); - buriedColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - buriedColour_actionPerformed(e); - } - }); + buriedColour.addActionListener(this); abovePIDColour.setLabel("Above % Identity"); userDefinedColour.setLabel("User Defined"); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - userDefinedColour_actionPerformed(e); - } - }); + userDefinedColour.addActionListener(this); PIDColour.setLabel("Percentage Identity"); - PIDColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - PIDColour_actionPerformed(e); - } - }); + PIDColour.addActionListener(this); BLOSUM62Colour.setLabel("BLOSUM62"); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - BLOSUM62Colour_actionPerformed(e); - } - }); + BLOSUM62Colour.addActionListener(this); conservationMenuItem.setLabel("Conservation"); + add(editMenu); + editMenu.add(copy); + copy.addActionListener(this); + editMenu.add(cut); + cut.addActionListener(this); + editMenu.add(toUpper); + toUpper.addActionListener(this); + editMenu.add(toLower); + toLower.addActionListener(this); + editMenu.add(toggleCase); + toggleCase.addActionListener(this); } void refresh() { - SequenceGroup sg = getGroup(); - SuperGroup superG = ap.av.alignment.getSuperGroup( sg ); - if( superG !=null) - superG.setSuperGroupProperties( sg ); - ap.seqPanel.seqCanvas.repaint(); + if(ap.overviewPanel!=null) + ap.overviewPanel.updateOverviewImage(); } - protected void clustalColour_actionPerformed(ActionEvent e) + protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth()); + sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth()); refresh(); } - protected void zappoColour_actionPerformed(ActionEvent e) + protected void zappoColour_actionPerformed() { getGroup().cs = new ZappoColourScheme(); refresh(); } - protected void taylorColour_actionPerformed(ActionEvent e) + protected void taylorColour_actionPerformed() { getGroup().cs = new TaylorColourScheme(); refresh(); } - - protected void hydrophobicityColour_actionPerformed(ActionEvent e) + protected void hydrophobicityColour_actionPerformed() { getGroup().cs = new HydrophobicColourScheme(); refresh(); } - protected void helixColour_actionPerformed(ActionEvent e) + protected void helixColour_actionPerformed() { getGroup().cs = new HelixColourScheme(); refresh(); } - protected void strandColour_actionPerformed(ActionEvent e) + protected void strandColour_actionPerformed() { getGroup().cs = new StrandColourScheme(); refresh(); } - protected void turnColour_actionPerformed(ActionEvent e) + protected void turnColour_actionPerformed() { getGroup().cs = new TurnColourScheme(); refresh(); } - protected void buriedColour_actionPerformed(ActionEvent e) + protected void buriedColour_actionPerformed() { getGroup().cs = new BuriedColourScheme(); refresh(); } - public void nucleotideMenuItem_actionPerformed(ActionEvent e) + public void nucleotideMenuItem_actionPerformed() { getGroup().cs = new NucleotideColourScheme(); refresh(); } - - - protected void abovePIDColour_itemStateChanged(ItemEvent ie) + protected void abovePIDColour_itemStateChanged() { SequenceGroup sg = getGroup(); + if(sg.cs==null) + return; + if (abovePIDColour.getState()) { - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, ap.av.alignment.getWidth())); - int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName()); - if (sg.cs instanceof ResidueColourScheme) - ( (ResidueColourScheme)sg. cs).setThreshold(threshold); - else if (sg.cs instanceof ScoreColourScheme) - ( (ScoreColourScheme) sg.cs).setThreshold(threshold); + int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, + getGroup().getName()); - SliderPanel.showPIDSlider(); + sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + SliderPanel.showPIDSlider(); } else // remove PIDColouring { - ResidueColourScheme rcs = (ResidueColourScheme) sg.cs; - rcs.setThreshold(0); - sg.cs = rcs; + sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); } refresh(); } - - protected void userDefinedColour_actionPerformed(ActionEvent e) + protected void userDefinedColour_actionPerformed() { - new UserDefinedColours( ap, getGroup()); + new UserDefinedColours(ap, getGroup()); } - protected void PIDColour_actionPerformed(ActionEvent e) + protected void PIDColour_actionPerformed() { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, - ap.av.alignment.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, + ap.av.alignment.getWidth())); refresh(); } - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + protected void BLOSUM62Colour_actionPerformed() { SequenceGroup sg = getGroup(); sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, - ap.av.alignment.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, + ap.av.alignment.getWidth())); refresh(); } - - protected void noColourmenuItem_actionPerformed(ActionEvent e) + protected void noColourmenuItem_actionPerformed() { getGroup().cs = null; refresh(); } - protected void conservationMenuItem_itemStateChanged(ItemEvent ie) + protected void conservationMenuItem_itemStateChanged() { SequenceGroup sg = getGroup(); + if(sg.cs==null) + return; - if(conservationMenuItem.getState()) + if (conservationMenuItem.getState()) { - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, - sg.sequences, 0, - ap.av.alignment.getWidth()); + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, + sg.getSequences(true), 0, + ap.av.alignment.getWidth()); - c.calculate(); - c.verdict(false, ap.av.ConsPercGaps); - ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); + c.calculate(); + c.verdict(false, ap.av.ConsPercGaps); + sg.cs.setConservation(c); - sg.cs = ccs; - - SliderPanel.setConservationSlider(ap, ccs, sg.getName()); + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); SliderPanel.showConservationSlider(); } else // remove ConservationColouring { - ConservationColourScheme ccs = (ConservationColourScheme)sg.cs; - sg.cs = ccs.cs; + sg.cs.setConservation(null); } - refresh(); + refresh(); } - protected void analyze_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300); - SequenceGroup sg = getGroup(); - StringBuffer sb = new StringBuffer(); - - for(int i=0; i