X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=206a969d106b2993521607c4f7883fdad9e01701;hb=35426f122a3db9e75360f2692c26a5452ec54460;hp=c2bf72934fdaec59b99f7341cde7d603f972de77;hpb=c97c8a9e4fd58a4927e040e314c5be3c5356745e;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index c2bf729..206a969 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -21,11 +21,9 @@ package jalview.gui; import MCview.*; import jalview.analysis.*; - import jalview.datamodel.*; - - import jalview.schemes.*; +import jalview.commands.ChangeCaseCommand; import java.awt.*; import java.awt.event.*; @@ -34,6 +32,8 @@ import javax.swing.*; import java.util.Vector; import jalview.io.FormatAdapter; +import javax.swing.event.ChangeListener; +import javax.swing.event.ChangeEvent; /** @@ -82,6 +82,9 @@ public class PopupMenu extends JPopupMenu JMenuItem enterPDB = new JMenuItem(); JMenuItem discoverPDB = new JMenuItem(); JMenu outputMenu = new JMenu(); + JMenuItem sequenceFeature = new JMenuItem(); + JMenuItem textColour = new JMenuItem(); + JMenu jMenu1 = new JMenu(); /** * Creates a new PopupMenu object. @@ -143,8 +146,7 @@ public class PopupMenu extends JPopupMenu if (seq != null) { - int start = Math.max(sequence.getName().length()-15, 0); - sequenceMenu.setText(sequence.getName().substring(start)); + sequenceMenu.setText(sequence.getName()); JMenuItem menuItem; if( seq.getDatasetSequence().getPDBId() != null) @@ -451,7 +453,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - upperCase_actionPerformed(e); + changeCase(e); } }); copy.setText("Copy"); @@ -467,7 +469,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - lowerCase_actionPerformed(e); + changeCase(e); } }); toggle.setText("Toggle Case"); @@ -475,7 +477,7 @@ public class PopupMenu extends JPopupMenu { public void actionPerformed(ActionEvent e) { - toggle_actionPerformed(e); + changeCase(e); } }); pdbMenu.setText("Associate Structure with Sequence"); @@ -504,21 +506,33 @@ public class PopupMenu extends JPopupMenu } }); outputMenu.setText("Output to Textbox..."); + sequenceFeature.setText("Create Sequence Feature"); + sequenceFeature.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceFeature_actionPerformed(e); + } + }); + textColour.setText("Text Colour"); + textColour.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + textColour_actionPerformed(e); + } + }); + jMenu1.setText("Group"); add(groupMenu); add(sequenceMenu); groupMenu.add(editMenu); groupMenu.add(outputMenu); - groupMenu.addSeparator(); - groupMenu.add(groupName); - groupMenu.add(unGroupMenuItem); - groupMenu.add(colourMenu); - groupMenu.add(showBoxes); - groupMenu.add(showText); - groupMenu.add(showColourText); - groupMenu.add(outline); - sequenceMenu.add(sequenceName); + groupMenu.add(sequenceFeature); + groupMenu.add(jMenu1); + sequenceMenu.add(sequenceName); sequenceMenu.add(pdbMenu); + colourMenu.add(textColour); colourMenu.add(noColourmenuItem); colourMenu.add(clustalColour); colourMenu.add(BLOSUM62Colour); @@ -565,6 +579,13 @@ public class PopupMenu extends JPopupMenu pdbMenu.add(pdbFromFile); pdbMenu.add(enterPDB); pdbMenu.add(discoverPDB); + jMenu1.add(groupName); + jMenu1.add(unGroupMenuItem); + jMenu1.add(colourMenu); + jMenu1.add(showBoxes); + jMenu1.add(showText); + jMenu1.add(showColourText); + jMenu1.add(outline); noColourmenuItem.setText("None"); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { @@ -805,9 +826,9 @@ public class PopupMenu extends JPopupMenu if (abovePIDColour.isSelected()) { - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(true), 0, - ap.av.alignment.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(true), sg.getStartRes(), + sg.getEndRes() + 1)); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName()); @@ -842,6 +863,7 @@ public class PopupMenu extends JPopupMenu sg.cs = udc; } + refresh(); } /** * DOCUMENT ME! @@ -852,8 +874,9 @@ public class PopupMenu extends JPopupMenu { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, - ap.av.alignment.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), + sg.getStartRes(), + sg.getEndRes() + 1)); refresh(); } @@ -868,8 +891,9 @@ public class PopupMenu extends JPopupMenu sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, - ap.av.alignment.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), + sg.getStartRes(), + sg.getEndRes() + 1)); refresh(); } @@ -900,8 +924,9 @@ public class PopupMenu extends JPopupMenu { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.getSequences(true), 0, - ap.av.alignment.getWidth()); + sg.getSequences(true), + sg.getStartRes(), + sg.getEndRes() + 1); c.calculate(); c.verdict(false, ap.av.ConsPercGaps); @@ -940,31 +965,6 @@ public class PopupMenu extends JPopupMenu groupName.setText(reply); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void analyze_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - JInternalFrame frame = new JInternalFrame(); - frame.setContentPane(cap); - Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300); - - SequenceGroup sg = getGroup(); - StringBuffer sb = new StringBuffer(); - - for (int i = 0; i < sg.getSize(false); i++) - { - Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i); - sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1)); - sb.append("\n"); - } - - sb.append("Something amazing will happen soon"); - cap.setText(sb.toString()); - } /** * DOCUMENT ME! @@ -1028,13 +1028,15 @@ public class PopupMenu extends JPopupMenu } s = s.replace(' ', '_'); - sequence.getDatasetSequence().setName(s); sequence.setName(s); ap.repaint(); } - sequence.getDatasetSequence().setDescription(description.getText()); sequence.setDescription(description.getText()); + + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + } /** @@ -1145,7 +1147,7 @@ public class PopupMenu extends JPopupMenu } else if(!representGroup) { - hseqs[index++] = sg.getSequenceAt(index); + hseqs[index++] = sg.getSequenceAt(i); } } @@ -1164,65 +1166,84 @@ public class PopupMenu extends JPopupMenu ap.alignFrame.cut_actionPerformed(null); } - public void upperCase_actionPerformed(ActionEvent e) - { - changeCase(e.getSource()); - } - - public void lowerCase_actionPerformed(ActionEvent e) - { - changeCase(e.getSource()); - } - - public void toggle_actionPerformed(ActionEvent e) - { - changeCase(e.getSource()); - } - - void changeCase(Object source) + void changeCase(ActionEvent e) { + Object source = e.getSource(); SequenceGroup sg = ap.av.getSelectionGroup(); + Vector regions = new Vector(); if (sg != null) { - for (int g = 0; g < sg.getSize(true); g++) + int start = sg.getStartRes(); + int end = sg.getEndRes() + 1; + + do { - int start = sg.getStartRes(); - int end = sg.getEndRes() + 1; + if (ap.av.hasHiddenColumns) + { + if(start==0) + start = ap.av.colSel.adjustForHiddenColumns(start); + + end = ap.av.colSel.getHiddenBoundaryRight(start); + if (start == end) + end = sg.getEndRes() + 1; + if (end > sg.getEndRes()) + end = sg.getEndRes() + 1; + } + + regions.addElement(new int[] + {start, end}); - do + if (ap.av.hasHiddenColumns) { - if (ap.av.hasHiddenColumns) - { - end = ap.av.colSel.getHiddenBoundaryRight(start); - if (start == end) - end = sg.getEndRes() + 1; - if (end > sg.getEndRes()) - end = sg.getEndRes() + 1; - } + start = ap.av.colSel.adjustForHiddenColumns(end); + start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1; + } + } + while (end < sg.getEndRes()); - if (source == toggle) - ( (SequenceI) sg.getSequences(true).elementAt(g)) - .toggleCase(start, end); - else - ( (SequenceI) sg.getSequences(true).elementAt(g)) - .changeCase(source == upperCase, start, end); + int[][] startEnd = new int[regions.size()][2]; + for (int i = 0; i < regions.size(); i++) + { + startEnd[i] = (int[]) regions.elementAt(i); + } - if (ap.av.hasHiddenColumns) - { - start = ap.av.colSel.adjustForHiddenColumns(end); - start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1; - } - } - while (end < sg.getEndRes()); + String description; + int caseChange; + + if(source==toggle) + { + description = "Toggle Case"; + caseChange = ChangeCaseCommand.TOGGLE_CASE; + } + else if(source==upperCase) + { + description = "To Upper Case"; + caseChange = ChangeCaseCommand.TO_UPPER; + } + else + { + description = "To Lower Case"; + caseChange = ChangeCaseCommand.TO_LOWER; } - PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); + + ChangeCaseCommand caseCommand = new ChangeCaseCommand( + description, sg.getSequencesAsArray(true), startEnd, caseChange + ); + + ap.alignFrame.addHistoryItem(caseCommand); + + + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + } } public void outputText_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(null); Desktop.addInternalFrame(cap, "Alignment output - " + e.getActionCommand(), 600, 500); @@ -1309,4 +1330,116 @@ public class PopupMenu extends JPopupMenu new jalview.io.DBRefFetcher( ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false); } + + public void sequenceFeature_actionPerformed(ActionEvent e) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if(sg==null) + return; + + int gSize= sg.getSize(false); + SequenceI [] seqs = new SequenceI[gSize]; + SequenceFeature [] features = new SequenceFeature[gSize]; + + for (int i = 0; i < gSize; i++) + { + seqs[i] = sg.getSequenceAt(i).getDatasetSequence(); + int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); + int end = sg.findEndRes(sg.getSequenceAt(i)); + features[i] = new SequenceFeature(null,null, null,start,end,"Jalview"); + } + + if (ap.seqPanel.seqCanvas.getFeatureRenderer() + .createNewFeatures(seqs, features)) + { + ap.alignFrame.showSeqFeatures.setSelected(true); + ap.av.setShowSequenceFeatures(true); + ap.highlightSearchResults(null); + } + } + + public void textColour_actionPerformed(ActionEvent e) + { + final SequenceGroup sg = getGroup(); + + int original1 = sg.textColour.getRGB(); + int original2 = sg.textColour2.getRGB(); + int thresh = sg.thresholdTextColour; + final JSlider slider = new JSlider(0, 750,sg.thresholdTextColour); + final JButton col1 = new JButton("DARK"); + col1.setBackground(sg.textColour); + col1.setForeground(sg.textColour); + final JButton col2 = new JButton("LIGHT"); + col2.setBackground(sg.textColour2); + col2.setForeground(sg.textColour2); + final JPanel bigpanel = new JPanel(new BorderLayout()); + JPanel panel = new JPanel(); + bigpanel.add(panel, BorderLayout.CENTER); + bigpanel.add(new JLabel( + "Select a dark and light text colour, then set the threshold to" + +"
switch between colours, based on background colour"), + BorderLayout.NORTH); + panel.add(col1); + panel.add(slider); + panel.add(col2); + + col1.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + Color col = JColorChooser.showDialog(bigpanel, + "Select Colour for Text", + sg.textColour); + if (col != null) + { + sg.textColour = col; + col1.setBackground(col); + col1.setForeground(col); + } + ap.repaint(); + } + }); + + col2.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + Color col = JColorChooser.showDialog(bigpanel, + "Select Colour for Text", + sg.textColour); + if (col != null) + { + sg.textColour2 = col; + col2.setBackground(col); + col2.setForeground(col); + } + ap.repaint(); + } + }); + + + slider.addChangeListener(new ChangeListener() + { + public void stateChanged(ChangeEvent evt) + { + sg.thresholdTextColour = slider.getValue(); + ap.repaint(); + } + }); + + int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop, + bigpanel, + "Adjust Foreground Text Colour Threshold", + JOptionPane.OK_CANCEL_OPTION, + JOptionPane.QUESTION_MESSAGE, + null, + null, null); + + if(reply==JOptionPane.CANCEL_OPTION) + { + sg.textColour = new Color(original1); + sg.textColour2 = new Color(original2); + sg.thresholdTextColour = thresh; + } + } }