X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=1ecf25453756a18794214d8b7281749fd5ed6a13;hb=b437b816507d2acc59e34f70a9cf8c7f81921681;hp=aceb508f03d06349392f39d8474344faccc7b8eb;hpb=9de867119284e37853a561a6965267d8c0487a4a;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index aceb508..1ecf254 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -229,8 +229,7 @@ public class AlignFrame extends Frame implements ActionListener, fr.setColour(type, ucs.findColour("A")); } - sf = new SequenceFeature(type, desc, "", start, end); - sf.setFeatureGroup(featureGroup); + sf = new SequenceFeature(type, desc, "", start, end, featureGroup); seq.addSequenceFeature(sf); } @@ -251,6 +250,13 @@ public class AlignFrame extends Frame implements ActionListener, public void keyPressed(KeyEvent evt) { + if (viewport.cursorMode + && evt.getKeyCode() >= KeyEvent.VK_0 + && evt.getKeyCode() <= KeyEvent.VK_9) + { + alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + } + switch (evt.getKeyCode()) { case 27: // escape key @@ -263,6 +269,10 @@ public class AlignFrame extends Frame implements ActionListener, } break; case KeyEvent.VK_C: + if (viewport.cursorMode) + { + alignPanel.seqPanel.setCursorColumn(); + } if (evt.isControlDown() || evt.isMetaDown()) { copy_actionPerformed(); @@ -281,21 +291,108 @@ public class AlignFrame extends Frame implements ActionListener, } break; case KeyEvent.VK_DOWN: - moveSelectedSequences(false); + if(viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0,1); + } + else + moveSelectedSequences(false); break; + case KeyEvent.VK_UP: - moveSelectedSequences(true); + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0,-1); + } + else + moveSelectedSequences(true); + break; + + case KeyEvent.VK_LEFT: + if(viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(-1,0); + } + break; + + case KeyEvent.VK_RIGHT: + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(1,0); + } + break; + case KeyEvent.VK_SPACE: + if(viewport.cursorMode) + { + alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()); + } + break; + + case KeyEvent.VK_DELETE: + case KeyEvent.VK_BACK_SPACE: + if(viewport.cursorMode) + { + alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()); + } + else + { + cut_actionPerformed(); + alignPanel.seqPanel.seqCanvas.repaint(); + } + break; + + case KeyEvent.VK_S: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRow(); + } + break; + case KeyEvent.VK_P: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorPosition(); + } + break; + + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRowAndColumn(); + } + break; + + case KeyEvent.VK_Q: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(true); + } break; + case KeyEvent.VK_M: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(false); + } + break; + + case KeyEvent.VK_F2: + viewport.cursorMode = ! viewport.cursorMode; + statusBar.setText("Keyboard editing mode is "+ + (viewport.cursorMode ? "on" : "off")); + if(viewport.cursorMode) + { + alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; + alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + } + alignPanel.seqPanel.seqCanvas.repaint(); + break; + case KeyEvent.VK_F: if (evt.isControlDown()) { findMenuItem_actionPerformed(); } break; - case KeyEvent.VK_BACK_SPACE: - case KeyEvent.VK_DELETE: - cut_actionPerformed(); - break; } } public void keyReleased(KeyEvent evt) @@ -336,6 +433,8 @@ public void itemStateChanged(ItemEvent evt) abovePIDThreshold_actionPerformed(); else if(evt.getSource()==applyToAllGroups) applyToAllGroups_actionPerformed(); + else if(evt.getSource()==autoCalculate) + viewport.autocalculateConsensus = autoCalculate.getState(); } public void actionPerformed(ActionEvent evt) { @@ -423,6 +522,8 @@ public void itemStateChanged(ItemEvent evt) PIDColour_actionPerformed(); else if(evt.getSource()==BLOSUM62Colour) BLOSUM62Colour_actionPerformed(); + else if(evt.getSource()==annotationColour) + new AnnotationColourChooser(viewport, alignPanel); else if(evt.getSource()==sortPairwiseMenuItem) sortPairwiseMenuItem_actionPerformed(); else if(evt.getSource()==sortIDMenuItem) @@ -828,6 +929,11 @@ public void itemStateChanged(ItemEvent evt) public void deselectAllSequenceMenuItem_actionPerformed() { + if(viewport.cursorMode) + { + alignPanel.seqPanel.keyboardNo1=null; + alignPanel.seqPanel.keyboardNo2=null; + } viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); @@ -1002,8 +1108,13 @@ public void itemStateChanged(ItemEvent evt) public void alignmentChanged() { - viewport.updateConsensus(); - viewport.updateConservation (); + viewport.alignment.padGaps(); + if(viewport.autocalculateConsensus) + { + viewport.updateConsensus(); + viewport.updateConservation(); + } + resetAllColourSchemes(); if(alignPanel.overviewPanel!=null) alignPanel.overviewPanel.updateOverviewImage(); @@ -1689,8 +1800,8 @@ public void itemStateChanged(ItemEvent evt) protected Menu colourMenu = new Menu("Colour"); protected Menu calculateMenu = new Menu("Calculate"); protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); - protected MenuItem deselectAllSequenceMenuItem = new MenuItem(); - protected MenuItem invertSequenceMenuItem = new MenuItem(); + protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); + protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); protected MenuItem remove2LeftMenuItem = new MenuItem(); protected MenuItem remove2RightMenuItem = new MenuItem(); protected MenuItem removeGappedColumnMenuItem = new MenuItem(); @@ -1748,6 +1859,8 @@ public void itemStateChanged(ItemEvent evt) protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); MenuItem modifyPID = new MenuItem(); MenuItem modifyConservation = new MenuItem(); + protected CheckboxMenuItem autoCalculate + = new CheckboxMenuItem("Autocalculate Consensus", true); protected Menu sortByTreeMenu = new Menu(); Menu sort = new Menu(); Menu calculate = new Menu(); @@ -1793,9 +1906,7 @@ public void itemStateChanged(ItemEvent evt) loadTree.addActionListener(this); selectAllSequenceMenuItem.addActionListener(this); - deselectAllSequenceMenuItem.setLabel("Deselect All"); deselectAllSequenceMenuItem.addActionListener(this); - invertSequenceMenuItem.setLabel("Invert Selection"); invertSequenceMenuItem.addActionListener(this); remove2LeftMenuItem.setLabel("Remove Left"); remove2LeftMenuItem.addActionListener(this); @@ -1927,6 +2038,7 @@ public void itemStateChanged(ItemEvent evt) sortByTreeMenu.setLabel("By Tree Order"); sort.setLabel("Sort"); calculate.setLabel("Calculate Tree"); + autoCalculate.addItemListener(this); inputText.setLabel("Input from textbox"); inputText.addActionListener(this); @@ -1944,6 +2056,8 @@ public void itemStateChanged(ItemEvent evt) sequenceFeatures.setLabel("Sequence Features"); sequenceFeatures.addItemListener(this); sequenceFeatures.setState(false); + annotationColour.setLabel("by Annotation..."); + annotationColour.addActionListener(this); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); @@ -2014,11 +2128,13 @@ public void itemStateChanged(ItemEvent evt) colourMenu.add(modifyConservation); colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); - calculateMenu.add(sort); + colourMenu.add(annotationColour); + calculateMenu.add(sort); calculateMenu.add(calculate); calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); calculateMenu.add(PCAMenuItem); + calculateMenu.add(autoCalculate); this.add(statusBar, BorderLayout.SOUTH); pasteMenu.add(pasteNew); pasteMenu.add(pasteThis); @@ -2103,6 +2219,7 @@ public void itemStateChanged(ItemEvent evt) viewPopup, colourPopup, calculatePopup, helpPopup; MenuItem featureSettings = new MenuItem(); CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); + MenuItem annotationColour = new MenuItem(); public void mousePressed(MouseEvent evt) {