/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
-\r
package jalview.appletgui;\r
\r
-import java.io.*;\r
import java.net.*;\r
import java.util.*;\r
\r
import java.awt.event.*;\r
\r
import jalview.analysis.*;\r
+import jalview.api.SequenceStructureBinding;\r
+import jalview.bin.JalviewLite;\r
import jalview.commands.*;\r
import jalview.datamodel.*;\r
import jalview.io.*;\r
import jalview.schemes.*;\r
+import jalview.structure.StructureSelectionManager;\r
\r
-public class AlignFrame\r
- extends Frame implements ActionListener,\r
- ItemListener, KeyListener, MouseListener\r
+public class AlignFrame extends EmbmenuFrame implements ActionListener,\r
+ ItemListener, KeyListener\r
{\r
public AlignmentPanel alignPanel;\r
+\r
public AlignViewport viewport;\r
+\r
int DEFAULT_WIDTH = 700;\r
+\r
int DEFAULT_HEIGHT = 500;\r
\r
String jalviewServletURL;\r
\r
- public AlignFrame(AlignmentI al,\r
- jalview.bin.JalviewLite applet,\r
- String title,\r
- boolean embedded)\r
+ public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,\r
+ String title, boolean embedded)\r
{\r
\r
if (applet != null)\r
try\r
{\r
jbInit();\r
- }\r
- catch (Exception ex)\r
+ } catch (Exception ex)\r
{\r
ex.printStackTrace();\r
}\r
viewport.updateConsensus(alignPanel);\r
\r
annotationPanelMenuItem.setState(viewport.showAnnotation);\r
+ displayNonconservedMenuItem.setState(viewport.getShowunconserved());\r
+ followMouseOverFlag.setState(viewport.getFollowHighlight());\r
+ showGroupConsensus.setState(viewport.showGroupConsensus);\r
+ showGroupConservation.setState(viewport.showGroupConservation);\r
+ showConsensusHistogram.setState(viewport.showConsensusHistogram);\r
+ showSequenceLogo.setState(viewport.showSequenceLogo);\r
\r
seqLimits.setState(viewport.showJVSuffix);\r
\r
{\r
sortPairwiseMenuItem_actionPerformed();\r
}\r
+ else if (param.equalsIgnoreCase("Length"))\r
+ {\r
+ sortLengthMenuItem_actionPerformed();\r
+ }\r
}\r
\r
param = applet.getParameter("wrap");\r
wrapMenuItem_actionPerformed();\r
}\r
}\r
-\r
+ param = applet.getParameter("centrecolumnlabels");\r
+ if (param != null)\r
+ {\r
+ centreColumnLabelFlag.setState(true);\r
+ centreColumnLabelFlag_stateChanged();\r
+ }\r
try\r
{\r
param = applet.getParameter("windowWidth");\r
int height = Integer.parseInt(param);\r
DEFAULT_HEIGHT = height;\r
}\r
+ } catch (Exception ex)\r
+ {\r
}\r
- catch (Exception ex)\r
- {}\r
\r
}\r
\r
- //Some JVMS send keyevents to Top frame or lowest panel,\r
- //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
+ // Some JVMS send keyevents to Top frame or lowest panel,\r
+ // Havent worked out why yet. So add to both this frame and seqCanvas for\r
+ // now\r
this.addKeyListener(this);\r
alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
alignPanel.idPanel.idCanvas.addKeyListener(this);\r
alignPanel.scalePanel.addKeyListener(this);\r
alignPanel.annotationPanel.addKeyListener(this);\r
+ alignPanel.annotationPanelHolder.addKeyListener(this);\r
+ alignPanel.annotationSpaceFillerHolder.addKeyListener(this);\r
+ alignPanel.alabels.addKeyListener(this);\r
+ createAlignFrameWindow(embedded, title);\r
\r
- if (embedded)\r
- {\r
- setEmbedded();\r
- }\r
- else\r
- {\r
- add(alignPanel, BorderLayout.CENTER);\r
- jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,\r
- DEFAULT_HEIGHT);\r
- }\r
- alignPanel.validate();\r
+ validate();\r
+ alignPanel.adjustAnnotationHeight();\r
alignPanel.paintAlignment(true);\r
}\r
\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param String DOCUMENT ME!\r
+ * \r
+ * @param String\r
+ * DOCUMENT ME!\r
*/\r
\r
public void parseFeaturesFile(String file, String type)\r
boolean featuresFile = false;\r
try\r
{\r
- featuresFile = new jalview.io.FeaturesFile(file,\r
- type).parse(viewport.alignment,\r
- alignPanel.seqPanel.seqCanvas.\r
- getFeatureRenderer().featureColours,\r
- featureLinks,\r
- true);\r
- }\r
- catch (Exception ex)\r
+ featuresFile = new jalview.io.FeaturesFile(file, type)\r
+ .parse(viewport.alignment,\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,\r
+ featureLinks, true, viewport.applet.getDefaultParameter("relaxedidmatch", false));\r
+ } catch (Exception ex)\r
{\r
ex.printStackTrace();\r
}\r
{\r
if (featureLinks.size() > 0)\r
{\r
- alignPanel.seqPanel.seqCanvas\r
- .getFeatureRenderer().featureLinks = featureLinks;\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;\r
}\r
viewport.showSequenceFeatures = true;\r
sequenceFeatures.setState(true);\r
+ if (viewport.featureSettings != null)\r
+ {\r
+ viewport.featureSettings.refreshTable();\r
+ }\r
alignPanel.paintAlignment(true);\r
}\r
\r
\r
public void keyPressed(KeyEvent evt)\r
{\r
- if (viewport.cursorMode &&\r
- ( (evt.getKeyCode() >= KeyEvent.VK_0 &&\r
- evt.getKeyCode() <= KeyEvent.VK_9)\r
- ||\r
- (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 &&\r
- evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)\r
- )\r
- && Character.isDigit(evt.getKeyChar()))\r
- alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
-\r
+ if (viewport.cursorMode\r
+ && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt\r
+ .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt\r
+ .getKeyCode() <= KeyEvent.VK_NUMPAD9))\r
+ && Character.isDigit(evt.getKeyChar()))\r
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
\r
switch (evt.getKeyCode())\r
{\r
- case 27: // escape key\r
- deselectAllSequenceMenuItem_actionPerformed();\r
- break;\r
- case KeyEvent.VK_X:\r
- if (evt.isControlDown() || evt.isMetaDown())\r
- {\r
- cut_actionPerformed();\r
- }\r
- break;\r
- case KeyEvent.VK_C:\r
- if (viewport.cursorMode && !evt.isControlDown())\r
- {\r
- alignPanel.seqPanel.setCursorColumn();\r
- }\r
- if (evt.isControlDown() || evt.isMetaDown())\r
- {\r
- copy_actionPerformed();\r
- }\r
- break;\r
- case KeyEvent.VK_V:\r
- if (evt.isControlDown())\r
- {\r
- paste(evt.isShiftDown());\r
- }\r
- break;\r
- case KeyEvent.VK_A:\r
- if (evt.isControlDown() || evt.isMetaDown())\r
- {\r
- selectAllSequenceMenuItem_actionPerformed();\r
- }\r
- break;\r
- case KeyEvent.VK_DOWN:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.moveCursor(0, 1);\r
- }\r
- else\r
- {\r
- moveSelectedSequences(false);\r
- }\r
- break;\r
+ case 27: // escape key\r
+ deselectAllSequenceMenuItem_actionPerformed();\r
+ \r
+ alignPanel.alabels.cancelDrag(); \r
+ break;\r
+ case KeyEvent.VK_X:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ cut_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_C:\r
+ if (viewport.cursorMode && !evt.isControlDown())\r
+ {\r
+ alignPanel.seqPanel.setCursorColumn();\r
+ }\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_V:\r
+ if (evt.isControlDown())\r
+ {\r
+ paste(evt.isShiftDown());\r
+ }\r
+ break;\r
+ case KeyEvent.VK_A:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_DOWN:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0, 1);\r
+ }\r
+ else\r
+ {\r
+ moveSelectedSequences(false);\r
+ }\r
+ break;\r
\r
- case KeyEvent.VK_UP:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.moveCursor(0, -1);\r
- }\r
- else\r
- {\r
- moveSelectedSequences(true);\r
- }\r
- break;\r
+ case KeyEvent.VK_UP:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0, -1);\r
+ }\r
+ else\r
+ {\r
+ moveSelectedSequences(true);\r
+ }\r
+ break;\r
\r
- case KeyEvent.VK_LEFT:\r
- if (evt.isAltDown() || !viewport.cursorMode)\r
- slideSequences(false,\r
- alignPanel.seqPanel.getKeyboardNo1());\r
- else\r
- alignPanel.seqPanel.moveCursor( -1, 0);\r
- break;\r
+ case KeyEvent.VK_LEFT:\r
+ if (evt.isAltDown() || !viewport.cursorMode)\r
+ slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());\r
+ else\r
+ alignPanel.seqPanel.moveCursor(-1, 0);\r
+ break;\r
\r
- case KeyEvent.VK_RIGHT:\r
- if (evt.isAltDown() || !viewport.cursorMode)\r
- slideSequences(true,\r
- alignPanel.seqPanel.getKeyboardNo1());\r
- else\r
- alignPanel.seqPanel.moveCursor( 1, 0);\r
- break;\r
+ case KeyEvent.VK_RIGHT:\r
+ if (evt.isAltDown() || !viewport.cursorMode)\r
+ slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());\r
+ else\r
+ alignPanel.seqPanel.moveCursor(1, 0);\r
+ break;\r
\r
- case KeyEvent.VK_SPACE:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()\r
- || evt.isShiftDown()\r
- || evt.isAltDown()\r
- );\r
- }\r
- break;\r
+ case KeyEvent.VK_SPACE:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()\r
+ || evt.isShiftDown() || evt.isAltDown());\r
+ }\r
+ break;\r
\r
- case KeyEvent.VK_DELETE:\r
- case KeyEvent.VK_BACK_SPACE:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
- || evt.isShiftDown()\r
- || evt.isAltDown());\r
- }\r
- else\r
- {\r
- cut_actionPerformed();\r
- alignPanel.seqPanel.seqCanvas.repaint();\r
- }\r
- break;\r
+ case KeyEvent.VK_DELETE:\r
+ case KeyEvent.VK_BACK_SPACE:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
+ || evt.isShiftDown() || evt.isAltDown());\r
+ }\r
+ else\r
+ {\r
+ cut_actionPerformed();\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ }\r
+ break;\r
\r
- case KeyEvent.VK_S:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.setCursorRow();\r
- }\r
- break;\r
- case KeyEvent.VK_P:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.setCursorPosition();\r
- }\r
- break;\r
+ case KeyEvent.VK_S:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRow();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_P:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorPosition();\r
+ }\r
+ break;\r
\r
- case KeyEvent.VK_ENTER:\r
- case KeyEvent.VK_COMMA:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.setCursorRowAndColumn();\r
- }\r
- break;\r
+ case KeyEvent.VK_ENTER:\r
+ case KeyEvent.VK_COMMA:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRowAndColumn();\r
+ }\r
+ break;\r
\r
- case KeyEvent.VK_Q:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
- }\r
- break;\r
- case KeyEvent.VK_M:\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
- }\r
- break;\r
+ case KeyEvent.VK_Q:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_M:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
+ }\r
+ break;\r
\r
- case KeyEvent.VK_F2:\r
- viewport.cursorMode = !viewport.cursorMode;\r
- statusBar.setText("Keyboard editing mode is " +\r
- (viewport.cursorMode ? "on" : "off"));\r
- if (viewport.cursorMode)\r
- {\r
- alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
- alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
- }\r
- break;\r
+ case KeyEvent.VK_F2:\r
+ viewport.cursorMode = !viewport.cursorMode;\r
+ statusBar.setText("Keyboard editing mode is "\r
+ + (viewport.cursorMode ? "on" : "off"));\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
+ }\r
+ break;\r
\r
- case KeyEvent.VK_F:\r
- if (evt.isControlDown())\r
- {\r
- findMenuItem_actionPerformed();\r
- }\r
- break;\r
+ case KeyEvent.VK_F:\r
+ if (evt.isControlDown())\r
+ {\r
+ findMenuItem_actionPerformed();\r
+ }\r
+ break;\r
\r
- case KeyEvent.VK_H:\r
+ case KeyEvent.VK_H:\r
+ {\r
+ boolean toggleSeqs = !evt.isControlDown();\r
+ boolean toggleCols = !evt.isShiftDown();\r
+ toggleHiddenRegions(toggleSeqs, toggleCols);\r
+ break;\r
+ }\r
+\r
+ case KeyEvent.VK_PAGE_UP:\r
+ if (viewport.wrapAlignment)\r
+ {\r
+ alignPanel.scrollUp(true);\r
+ }\r
+ else\r
{\r
- boolean toggleSeqs = !evt.isControlDown();\r
- boolean toggleCols = !evt.isShiftDown();\r
- boolean hide = false;\r
- SequenceGroup sg = viewport.getSelectionGroup();\r
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq\r
+ - viewport.endSeq + viewport.startSeq);\r
+ }\r
+ break;\r
\r
- if (toggleSeqs)\r
- {\r
- if (sg != null && sg.getSize() != viewport.alignment.getHeight())\r
- {\r
- hide = true;\r
- viewport.hideAllSelectedSeqs();\r
- }\r
- else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))\r
- {\r
- viewport.showAllHiddenSeqs();\r
- }\r
- }\r
+ case KeyEvent.VK_PAGE_DOWN:\r
+ if (viewport.wrapAlignment)\r
+ {\r
+ alignPanel.scrollUp(false);\r
+ }\r
+ else\r
+ {\r
+ alignPanel.setScrollValues(viewport.startRes, viewport.startSeq\r
+ + viewport.endSeq - viewport.startSeq);\r
+ }\r
+ break;\r
\r
- if (toggleCols)\r
- {\r
- if (viewport.colSel.getSelected().size() > 0)\r
- {\r
- viewport.hideSelectedColumns();\r
- if (!toggleSeqs)\r
- {\r
- viewport.selectionGroup = sg;\r
- }\r
- }\r
- else if (!hide)\r
- {\r
- viewport.showAllHiddenColumns();\r
- }\r
- }\r
- break;\r
+ case KeyEvent.VK_Z:\r
+ if (evt.isControlDown())\r
+ {\r
+ undoMenuItem_actionPerformed();\r
}\r
+ break;\r
\r
- case KeyEvent.VK_PAGE_UP:\r
- if (viewport.wrapAlignment)\r
+ case KeyEvent.VK_Y:\r
+ if (evt.isControlDown())\r
+ {\r
+ redoMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_L:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(true);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_R:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_E:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isShiftDown())\r
{\r
- alignPanel.scrollUp(true);\r
+ this.removeAllGapsMenuItem_actionPerformed();\r
}\r
else\r
{\r
- alignPanel.setScrollValues(viewport.startRes,\r
- viewport.startSeq\r
- - viewport.endSeq + viewport.startSeq);\r
+ removeGappedColumnMenuItem_actionPerformed();\r
}\r
- break;\r
-\r
- case KeyEvent.VK_PAGE_DOWN:\r
- if (viewport.wrapAlignment)\r
+ }\r
+ break;\r
+ case KeyEvent.VK_I:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isAltDown())\r
{\r
- alignPanel.scrollUp(false);\r
+ invertColSel_actionPerformed();\r
}\r
else\r
{\r
- alignPanel.setScrollValues(viewport.startRes,\r
- viewport.startSeq\r
- + viewport.endSeq - viewport.startSeq);\r
+ invertSequenceMenuItem_actionPerformed();\r
}\r
- break;\r
+ }\r
+ break;\r
\r
- case KeyEvent.VK_Z:\r
- if (evt.isControlDown())\r
- {\r
- undoMenuItem_actionPerformed();\r
- }\r
- break;\r
+ case KeyEvent.VK_U:\r
+ if (evt.isControlDown())\r
+ {\r
+ this.deleteGroups_actionPerformed();\r
+ }\r
+ break;\r
\r
- case KeyEvent.VK_Y:\r
- if (evt.isControlDown())\r
- {\r
- redoMenuItem_actionPerformed();\r
- }\r
- break;\r
+ case KeyEvent.VK_T:\r
+ if (evt.isControlDown())\r
+ {\r
+ newView(null);\r
+ }\r
+ break;\r
\r
- case KeyEvent.VK_L:\r
- if (evt.isControlDown())\r
- {\r
- trimAlignment(true);\r
- }\r
- break;\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ }\r
\r
- case KeyEvent.VK_R:\r
- if (evt.isControlDown())\r
+ /**\r
+ * called by key handler and the hide all/show all menu items\r
+ * \r
+ * @param toggleSeqs\r
+ * @param toggleCols\r
+ */\r
+ private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)\r
+ {\r
+ boolean hide = false;\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ if (!toggleSeqs && !toggleCols)\r
+ {\r
+ // Hide everything by the current selection - this is a hack - we do the\r
+ // invert and then hide\r
+ // first check that there will be visible columns after the invert.\r
+ if ((viewport.colSel != null && viewport.colSel.getSelected() != null && viewport.colSel\r
+ .getSelected().size() > 0)\r
+ || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg\r
+ .getEndRes()))\r
+ {\r
+ // now invert the sequence set, if required - empty selection implies\r
+ // that no hiding is required.\r
+ if (sg != null)\r
{\r
- trimAlignment(false);\r
- }\r
- break;\r
+ invertSequenceMenuItem_actionPerformed();\r
+ sg = viewport.getSelectionGroup();\r
+ toggleSeqs = true;\r
\r
- case KeyEvent.VK_E:\r
- if (evt.isControlDown())\r
- {\r
- if (evt.isShiftDown())\r
- {\r
- this.removeAllGapsMenuItem_actionPerformed();\r
- }\r
- else\r
- {\r
- removeGappedColumnMenuItem_actionPerformed();\r
- }\r
- }\r
- break;\r
- case KeyEvent.VK_I:\r
- if (evt.isControlDown())\r
- {\r
- if (evt.isAltDown())\r
- {\r
- viewport.invertColumnSelection();\r
- }\r
- else\r
- {\r
- this.invertSequenceMenuItem_actionPerformed();\r
- }\r
}\r
- break;\r
+ viewport.expandColSelection(sg, true);\r
+ // finally invert the column selection and get the new sequence\r
+ // selection and indicate it should be hidden.\r
+ invertColSel_actionPerformed();\r
+ toggleCols = true;\r
+ }\r
+ }\r
\r
- case KeyEvent.VK_U:\r
- if (evt.isControlDown())\r
- {\r
- this.deleteGroups_actionPerformed();\r
- }\r
- break;\r
+ if (toggleSeqs)\r
+ {\r
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())\r
+ {\r
+ hide = true;\r
+ viewport.hideAllSelectedSeqs();\r
+ }\r
+ else if (!(toggleCols && viewport.colSel.getSelected().size() > 0))\r
+ {\r
+ viewport.showAllHiddenSeqs();\r
+ }\r
+ }\r
\r
- case KeyEvent.VK_T:\r
- if (evt.isControlDown())\r
+ if (toggleCols)\r
+ {\r
+ if (viewport.colSel.getSelected().size() > 0)\r
+ {\r
+ viewport.hideSelectedColumns();\r
+ if (!toggleSeqs)\r
{\r
- newView();\r
+ viewport.selectionGroup = sg;\r
}\r
- break;\r
-\r
+ }\r
+ else if (!hide)\r
+ {\r
+ viewport.showAllHiddenColumns();\r
+ }\r
}\r
- alignPanel.paintAlignment(true);\r
}\r
\r
public void keyReleased(KeyEvent evt)\r
- {}\r
+ {\r
+ }\r
\r
public void keyTyped(KeyEvent evt)\r
- {}\r
+ {\r
+ }\r
\r
public void itemStateChanged(ItemEvent evt)\r
{\r
- if (evt.getSource() == colourTextMenuItem)\r
+ if (evt.getSource() == displayNonconservedMenuItem)\r
+ {\r
+ displayNonconservedMenuItem_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == colourTextMenuItem)\r
{\r
colourTextMenuItem_actionPerformed();\r
}\r
{\r
viewport.autocalculateConsensus = autoCalculate.getState();\r
}\r
-\r
+ else if (evt.getSource() == sortByTree)\r
+ {\r
+ viewport.sortByTree = sortByTree.getState();\r
+ }\r
+ else if (evt.getSource() == this.centreColumnLabelFlag)\r
+ {\r
+ centreColumnLabelFlag_stateChanged();\r
+ }\r
+ else if (evt.getSource() == this.followMouseOverFlag)\r
+ {\r
+ mouseOverFlag_stateChanged();\r
+ }\r
+ else if (evt.getSource() == showGroupConsensus)\r
+ {\r
+ showGroupConsensus_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == showGroupConservation)\r
+ {\r
+ showGroupConservation_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == showSequenceLogo)\r
+ {\r
+ showSequenceLogo_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == showConsensusHistogram)\r
+ {\r
+ showConsensusHistogram_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == applyAutoAnnotationSettings)\r
+ {\r
+ applyAutoAnnotationSettings_actionPerformed();\r
+ }\r
alignPanel.paintAlignment(true);\r
}\r
\r
+ private void mouseOverFlag_stateChanged()\r
+ {\r
+ viewport.followHighlight = followMouseOverFlag.getState();\r
+ // TODO: could kick the scrollTo mechanism to reset view for current\r
+ // searchresults.\r
+ }\r
+\r
+ private void centreColumnLabelFlag_stateChanged()\r
+ {\r
+ viewport.centreColumnLabels = centreColumnLabelFlag.getState();\r
+ this.alignPanel.annotationPanel.repaint();\r
+ }\r
+\r
public void actionPerformed(ActionEvent evt)\r
{\r
Object source = evt.getSource();\r
{\r
delete_actionPerformed();\r
}\r
+ else if (source == grpsFromSelection)\r
+ {\r
+ makeGrpsFromSelection_actionPerformed();\r
+ }\r
else if (source == deleteGroups)\r
{\r
deleteGroups_actionPerformed();\r
}\r
else if (source == newView)\r
{\r
- newView();\r
+ newView(null);\r
}\r
else if (source == showColumns)\r
{\r
else if (source == showSeqs)\r
{\r
viewport.showAllHiddenSeqs();\r
+ alignPanel.paintAlignment(true);\r
}\r
else if (source == hideColumns)\r
{\r
viewport.hideSelectedColumns();\r
alignPanel.paintAlignment(true);\r
}\r
- else if (source == hideSequences && viewport.getSelectionGroup() != null)\r
+ else if (source == hideSequences\r
+ && viewport.getSelectionGroup() != null)\r
+ {\r
+ viewport.hideAllSelectedSeqs();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == hideAllButSelection)\r
+ {\r
+ toggleHiddenRegions(false, false);\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == hideAllSelection)\r
{\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+ viewport.expandColSelection(sg, false);\r
viewport.hideAllSelectedSeqs();\r
+ viewport.hideSelectedColumns();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == showAllHidden)\r
+ {\r
+ viewport.showAllHiddenColumns();\r
+ viewport.showAllHiddenSeqs();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == showGroupConsensus)\r
+ {\r
+ showGroupConsensus_actionPerformed();\r
+ }\r
+ else if (source == showGroupConservation)\r
+ {\r
+ showGroupConservation_actionPerformed();\r
+ }\r
+ else if (source == showSequenceLogo)\r
+ {\r
+ showSequenceLogo_actionPerformed();\r
+ }\r
+ else if (source == showConsensusHistogram)\r
+ {\r
+ showConsensusHistogram_actionPerformed();\r
+ }\r
+ else if (source == applyAutoAnnotationSettings)\r
+ {\r
+ applyAutoAnnotationSettings_actionPerformed();\r
}\r
else if (source == featureSettings)\r
{\r
new FeatureSettings(alignPanel);\r
}\r
- else if(source== alProperties)\r
+ else if (source == alProperties)\r
{\r
- StringBuffer contents = new StringBuffer();\r
-\r
- float avg = 0;\r
- int min=Integer.MAX_VALUE, max=0;\r
- for(int i=0; i<viewport.alignment.getHeight(); i++)\r
- {\r
- int size = viewport.alignment.getSequenceAt(i).getEnd()\r
- -viewport.alignment.getSequenceAt(i).getStart();\r
- avg += size;\r
- if(size>max)\r
- max = size;\r
- if(size<min)\r
- min = size;\r
- }\r
- avg = avg/(float)viewport.alignment.getHeight();\r
-\r
- contents.append("\nSequences: "+ viewport.alignment.getHeight());\r
- contents.append("\nMinimum Sequence Length: "+min);\r
- contents.append("\nMaximum Sequence Length: "+max);\r
- contents.append("\nAverage Length: "+(int)avg);\r
-\r
- if (((Alignment)viewport.alignment).alignmentProperties != null)\r
- {\r
- Hashtable props = ((Alignment)viewport.alignment).alignmentProperties;\r
- Enumeration en = props.keys();\r
- while(en.hasMoreElements())\r
- {\r
- String key = en.nextElement().toString();\r
- contents.append("\n"+key+"\t"+props.get(key));\r
- }\r
- }\r
-\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
- cap.setText(contents.toString());\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame,\r
- "Alignment Properties: "+getTitle()\r
- , 400, 250);\r
+ StringBuffer contents = new jalview.io.AlignmentProperties(\r
+ viewport.alignment).formatAsString();\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ cap.setText(contents.toString());\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "\r
+ + getTitle(), 400, 250);\r
}\r
else if (source == overviewMenuItem)\r
{\r
else if (source == clustalColour)\r
{\r
abovePIDThreshold.setState(false);\r
- changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
- viewport.alignment.getWidth()));\r
+ changeColour(new ClustalxColourScheme(\r
+ viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth()));\r
}\r
else if (source == zappoColour)\r
{\r
{\r
sortIDMenuItem_actionPerformed();\r
}\r
+ else if (source == sortLengthMenuItem)\r
+ {\r
+ sortLengthMenuItem_actionPerformed();\r
+ }\r
else if (source == sortGroupMenuItem)\r
{\r
sortGroupMenuItem_actionPerformed();\r
Frame frame = new Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame,\r
- "Alignment output - " + e.getActionCommand(),\r
- 600, 500);\r
- cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
- viewport.getAlignment(),\r
- viewport.showJVSuffix));\r
+ "Alignment output - " + e.getActionCommand(), 600, 500);\r
+ cap.setText(new AppletFormatAdapter().formatSequences(\r
+ e.getActionCommand(), viewport.getAlignment(),\r
+ viewport.showJVSuffix));\r
}\r
\r
public void loadAnnotations()\r
public String outputAnnotations(boolean displayTextbox)\r
{\r
String annotation = new AnnotationFile().printAnnotations(\r
- viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,\r
- viewport.alignment.getGroups(),\r
- ((Alignment) viewport.alignment).alignmentProperties);\r
+ viewport.showAnnotation ? viewport.alignment\r
+ .getAlignmentAnnotation() : null, viewport.alignment\r
+ .getGroups(),\r
+ ((Alignment) viewport.alignment).alignmentProperties);\r
\r
if (displayTextbox)\r
{\r
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
Frame frame = new Frame();\r
frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame,\r
- "Annotations",\r
- 600, 500);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);\r
cap.setText(annotation);\r
}\r
\r
return annotation;\r
}\r
\r
+ private Hashtable getDisplayedFeatureCols()\r
+ {\r
+ if (alignPanel.getFeatureRenderer() != null && viewport.featuresDisplayed!=null)\r
+ {\r
+ FeatureRenderer fr = alignPanel.getFeatureRenderer();\r
+ Hashtable fcols = new Hashtable();\r
+ Enumeration en = viewport.featuresDisplayed.keys();\r
+ while (en.hasMoreElements())\r
+ {\r
+ Object col = en.nextElement();\r
+ fcols.put(col, fr.featureColours.get(col));\r
+ }\r
+ return fcols;\r
+ }\r
+ return null;\r
+ }\r
+\r
public String outputFeatures(boolean displayTextbox, String format)\r
{\r
String features;\r
if (format.equalsIgnoreCase("Jalview"))\r
{\r
features = new FeaturesFile().printJalviewFormat(\r
- viewport.alignment.getSequencesArray(),\r
- viewport.featuresDisplayed);\r
+ viewport.alignment.getSequencesArray(),\r
+ getDisplayedFeatureCols());\r
}\r
else\r
{\r
features = new FeaturesFile().printGFFFormat(\r
- viewport.alignment.getSequencesArray(),\r
- viewport.featuresDisplayed);\r
+ viewport.alignment.getSequencesArray(),\r
+ getDisplayedFeatureCols());\r
}\r
\r
if (displayTextbox)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ boolean frimport=false;\r
+ if (features==null || features.equals("No Features Visible"))\r
+ {\r
+ features = "# No features visible - paste some and import them here.";\r
+ frimport=true;\r
+ }\r
+ \r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);\r
+ if (frimport)\r
+ {\r
+ cap.setAnnotationImport();\r
+ }\r
Frame frame = new Frame();\r
frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame,\r
- "Features",\r
- 600, 500);\r
-\r
+ jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);\r
cap.setText(features);\r
+ } else {\r
+ if (features==null)\r
+ features = "";\r
}\r
\r
return features;\r
{\r
StringBuffer url = new StringBuffer(jalviewServletURL);\r
\r
- url.append("?open=" +\r
- appendProtocol(viewport.applet.getParameter("file")));\r
+ url.append("?open="\r
+ + appendProtocol(viewport.applet.getParameter("file")));\r
\r
if (viewport.applet.getParameter("features") != null)\r
{\r
\r
if (viewport.applet.getParameter("defaultColour") != null)\r
{\r
- url.append("&colour=" +\r
- removeWhiteSpace(viewport.applet.getParameter("defaultColour"))\r
- );\r
+ url.append("&colour="\r
+ + removeWhiteSpace(viewport.applet\r
+ .getParameter("defaultColour")));\r
}\r
\r
if (viewport.applet.getParameter("userDefinedColour") != null)\r
{\r
- url.append("&colour=" +\r
- removeWhiteSpace(viewport.applet.getParameter(\r
- "userDefinedColour"))\r
- );\r
+ url.append("&colour="\r
+ + removeWhiteSpace(viewport.applet\r
+ .getParameter("userDefinedColour")));\r
+ }\r
+ if (viewport.applet.getParameter("tree") != null)\r
+ {\r
+ url.append("&tree="\r
+ + appendProtocol(viewport.applet.getParameter("tree")));\r
+ }\r
+ if (viewport.applet.getParameter("treeFile") != null)\r
+ {\r
+ url.append("&tree="\r
+ + appendProtocol(viewport.applet.getParameter("treeFile")));\r
}\r
\r
showURL(url.toString(), "FULL_APP");\r
try\r
{\r
new URL(url);\r
+ url = URLEncoder.encode(url);\r
}\r
+ /*\r
+ * When we finally deprecate 1.1 compatibility, we can start to use\r
+ * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch\r
+ * (UnsupportedEncodingException ex) { System.err.println("WARNING -\r
+ * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);\r
+ * ex.printStackTrace(); }\r
+ */\r
catch (java.net.MalformedURLException ex)\r
{\r
url = viewport.applet.getCodeBase() + url;\r
if (PaintRefresher.components.size() == 0 && viewport.applet == null)\r
{\r
System.exit(0);\r
+ } else {\r
}\r
-\r
+ viewport = null;\r
+ alignPanel = null;\r
this.dispose();\r
}\r
\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void undoMenuItem_actionPerformed()\r
{\r
\r
CommandI command = (CommandI) viewport.historyList.pop();\r
viewport.redoList.push(command);\r
- command.undoCommand();\r
+ command.undoCommand(null);\r
\r
AlignViewport originalSource = getOriginatingSource(command);\r
\r
originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
updateEditMenuBar();\r
originalSource.firePropertyChange("alignment", null,\r
- originalSource.alignment.getSequences());\r
+ originalSource.alignment.getSequences());\r
}\r
\r
/**\r
* DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
+ * \r
+ * @param e\r
+ * DOCUMENT ME!\r
*/\r
protected void redoMenuItem_actionPerformed()\r
{\r
\r
CommandI command = (CommandI) viewport.redoList.pop();\r
viewport.historyList.push(command);\r
- command.doCommand();\r
+ command.doCommand(null);\r
\r
AlignViewport originalSource = getOriginatingSource(command);\r
originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
\r
updateEditMenuBar();\r
originalSource.firePropertyChange("alignment", null,\r
- originalSource.alignment.getSequences());\r
+ originalSource.alignment.getSequences());\r
}\r
\r
AlignViewport getOriginatingSource(CommandI command)\r
{\r
AlignViewport originalSource = null;\r
- //For sequence removal and addition, we need to fire\r
- //the property change event FROM the viewport where the\r
- //original alignment was altered\r
+ // For sequence removal and addition, we need to fire\r
+ // the property change event FROM the viewport where the\r
+ // original alignment was altered\r
AlignmentI al = null;\r
if (command instanceof EditCommand)\r
{\r
EditCommand editCommand = (EditCommand) command;\r
al = editCommand.getAlignment();\r
- Vector comps = (Vector) PaintRefresher.components\r
- .get(viewport.getSequenceSetId());\r
+ Vector comps = (Vector) PaintRefresher.components.get(viewport\r
+ .getSequenceSetId());\r
for (int i = 0; i < comps.size(); i++)\r
{\r
if (comps.elementAt(i) instanceof AlignmentPanel)\r
{\r
- if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)\r
+ if (al == ((AlignmentPanel) comps.elementAt(i)).av.alignment)\r
{\r
- originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;\r
+ originalSource = ((AlignmentPanel) comps.elementAt(i)).av;\r
break;\r
}\r
}\r
\r
if (originalSource == null)\r
{\r
- //The original view is closed, we must validate\r
- //the current view against the closed view first\r
+ // The original view is closed, we must validate\r
+ // the current view against the closed view first\r
if (al != null)\r
{\r
PaintRefresher.validateSequences(al, viewport.alignment);\r
synchronized void slideSequences(boolean right, int size)\r
{\r
Vector sg = new Vector();\r
- if(viewport.cursorMode)\r
+ if (viewport.cursorMode)\r
+ {\r
+ sg.addElement(viewport.alignment\r
+ .getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));\r
+ }\r
+ else if (viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().getSize() != viewport.alignment\r
+ .getHeight())\r
{\r
- sg.addElement(viewport.alignment.getSequenceAt(\r
- alignPanel.seqPanel.seqCanvas.cursorY));\r
+ sg = viewport.getSelectionGroup().getSequences(\r
+ viewport.hiddenRepSequences);\r
}\r
- else if(viewport.getSelectionGroup()!=null\r
- && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())\r
- {\r
- sg = viewport.getSelectionGroup().getSequences(\r
- viewport.hiddenRepSequences);\r
- }\r
\r
- if(sg.size()<1)\r
+ if (sg.size() < 1)\r
{\r
return;\r
}\r
\r
for (int i = 0; i < viewport.alignment.getHeight(); i++)\r
{\r
- if(!sg.contains(viewport.alignment.getSequenceAt(i)))\r
- invertGroup.addElement(viewport.alignment.getSequenceAt(i));\r
+ if (!sg.contains(viewport.alignment.getSequenceAt(i)))\r
+ invertGroup.addElement(viewport.alignment.getSequenceAt(i));\r
}\r
\r
SequenceI[] seqs1 = new SequenceI[sg.size()];\r
\r
SlideSequencesCommand ssc;\r
if (right)\r
- ssc = new SlideSequencesCommand("Slide Sequences",\r
- seqs2, seqs1, size,\r
- viewport.getGapCharacter()\r
- );\r
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,\r
+ size, viewport.getGapCharacter());\r
else\r
- ssc = new SlideSequencesCommand("Slide Sequences",\r
- seqs1, seqs2, size,\r
- viewport.getGapCharacter()\r
- );\r
+ ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,\r
+ size, viewport.getGapCharacter());\r
\r
int groupAdjustment = 0;\r
if (ssc.getGapsInsertedBegin() && right)\r
else if (!ssc.getGapsInsertedBegin() && !right)\r
{\r
if (viewport.cursorMode)\r
- alignPanel.seqPanel.moveCursor( -size, 0);\r
+ alignPanel.seqPanel.moveCursor(-size, 0);\r
else\r
groupAdjustment = -size;\r
}\r
if (groupAdjustment != 0)\r
{\r
viewport.getSelectionGroup().setStartRes(\r
- viewport.getSelectionGroup().getStartRes() + groupAdjustment);\r
+ viewport.getSelectionGroup().getStartRes() + groupAdjustment);\r
viewport.getSelectionGroup().setEndRes(\r
- viewport.getSelectionGroup().getEndRes() + groupAdjustment);\r
+ viewport.getSelectionGroup().getEndRes() + groupAdjustment);\r
}\r
\r
-\r
boolean appendHistoryItem = false;\r
- if(viewport.historyList!=null\r
- && viewport.historyList.size()>0\r
- && viewport.historyList.peek() instanceof SlideSequencesCommand)\r
+ if (viewport.historyList != null && viewport.historyList.size() > 0\r
+ && viewport.historyList.peek() instanceof SlideSequencesCommand)\r
{\r
- appendHistoryItem = ssc.appendSlideCommand(\r
- (SlideSequencesCommand)viewport.historyList.peek())\r
- ;\r
+ appendHistoryItem = ssc\r
+ .appendSlideCommand((SlideSequencesCommand) viewport.historyList\r
+ .peek());\r
}\r
\r
- if(!appendHistoryItem)\r
+ if (!appendHistoryItem)\r
addHistoryItem(ssc);\r
\r
repaint();\r
}\r
\r
static StringBuffer copiedSequences;\r
+\r
static Vector copiedHiddenColumns;\r
+\r
protected void copy_actionPerformed()\r
{\r
if (viewport.getSelectionGroup() == null)\r
{\r
copiedHiddenColumns = new Vector();\r
int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
- for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();\r
- i++)\r
+ for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()\r
+ .size(); i++)\r
{\r
- int[] region = (int[])\r
- viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
+ int[] region = (int[]) viewport.getColumnSelection()\r
+ .getHiddenColumns().elementAt(i);\r
\r
copiedHiddenColumns.addElement(new int[]\r
- {region[0] - hiddenOffset,\r
- region[1] - hiddenOffset});\r
+ { region[0] - hiddenOffset, region[1] - hiddenOffset });\r
}\r
}\r
else\r
}\r
}\r
\r
- //FIND START RES\r
- //Returns residue following index if gap\r
+ // FIND START RES\r
+ // Returns residue following index if gap\r
startRes = seq.findPosition(sg.getStartRes());\r
\r
- //FIND END RES\r
- //Need to find the residue preceeding index if gap\r
+ // FIND END RES\r
+ // Need to find the residue preceeding index if gap\r
endRes = 0;\r
\r
for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)\r
{\r
ch = seq.getCharAt(j);\r
- if (!jalview.util.Comparison.isGap( (ch)))\r
+ if (!jalview.util.Comparison.isGap((ch)))\r
{\r
endRes++;\r
}\r
endRes += seq.getStart() - 1;\r
}\r
\r
- copiedSequences.append(seq.getName() + "\t" +\r
- startRes + "\t" +\r
- endRes + "\t" +\r
- seq.getSequenceAsString(sg.getStartRes(),\r
- sg.getEndRes() + 1) + "\n");\r
+ copiedSequences.append(seq.getName()\r
+ + "\t"\r
+ + startRes\r
+ + "\t"\r
+ + endRes\r
+ + "\t"\r
+ + seq.getSequenceAsString(sg.getStartRes(),\r
+ sg.getEndRes() + 1) + "\n");\r
}\r
\r
}\r
newtitle = newtitle.concat("- from " + getTitle());\r
}\r
AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
- viewport.applet,\r
- newtitle,\r
- false);\r
+ viewport.applet, newtitle, false);\r
if (copiedHiddenColumns != null)\r
{\r
for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
}\r
\r
jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,\r
- DEFAULT_HEIGHT);\r
+ DEFAULT_HEIGHT);\r
}\r
else\r
{\r
addSequences(newSeqs);\r
}\r
\r
- }\r
- catch (Exception ex)\r
- {} // could be anything being pasted in here\r
+ } catch (Exception ex)\r
+ {\r
+ } // could be anything being pasted in here\r
\r
}\r
\r
viewport.alignment.addSequence(seqs[i]);\r
}\r
\r
- //!newAlignment\r
- addHistoryItem(new EditCommand(\r
- "Add sequences",\r
- EditCommand.PASTE,\r
- seqs,\r
- 0,\r
- viewport.alignment.getWidth(),\r
- viewport.alignment)\r
- );\r
+ // !newAlignment\r
+ addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,\r
+ seqs, 0, viewport.alignment.getWidth(), viewport.alignment));\r
\r
viewport.setEndSeq(viewport.alignment.getHeight());\r
viewport.alignment.getWidth();\r
viewport.firePropertyChange("alignment", null,\r
- viewport.alignment.getSequences());\r
+ viewport.alignment.getSequences());\r
\r
}\r
\r
if (sg.getSize() == viewport.alignment.getHeight())\r
{\r
viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
+ sg.getEndRes() + 1);\r
}\r
\r
SequenceI[] cut = new SequenceI[seqs.size()];\r
}\r
\r
/*\r
- //ADD HISTORY ITEM\r
+ * //ADD HISTORY ITEM\r
*/\r
- addHistoryItem(new EditCommand("Cut Sequences",\r
- EditCommand.CUT,\r
- cut,\r
- sg.getStartRes(),\r
- sg.getEndRes() - sg.getStartRes() + 1,\r
- viewport.alignment));\r
+ addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,\r
+ sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,\r
+ viewport.alignment));\r
\r
viewport.setSelectionGroup(null);\r
viewport.alignment.deleteGroup(sg);\r
\r
- viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+ .getSequences());\r
\r
if (viewport.getAlignment().getHeight() < 1)\r
{\r
this.setVisible(false);\r
}\r
+ viewport.sendSelection();\r
+ }\r
+\r
+ /**\r
+ * group consensus toggled\r
+ * \r
+ */\r
+ protected void showGroupConsensus_actionPerformed()\r
+ {\r
+ viewport.setShowGroupConsensus(showGroupConsensus.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+\r
+ }\r
+\r
+ /**\r
+ * group conservation toggled.\r
+ */\r
+ protected void showGroupConservation_actionPerformed()\r
+ {\r
+ viewport.setShowGroupConservation(showGroupConservation.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt\r
+ * .event.ActionEvent)\r
+ */\r
+ protected void showConsensusHistogram_actionPerformed()\r
+ {\r
+ viewport.setShowConsensusHistogram(showConsensusHistogram.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
+ * @see\r
+ * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt\r
+ * .event.ActionEvent)\r
+ */\r
+ protected void showSequenceLogo_actionPerformed()\r
+ {\r
+ viewport.setShowSequenceLogo(showSequenceLogo.getState());\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ protected void applyAutoAnnotationSettings_actionPerformed()\r
+ {\r
+ alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());\r
+ }\r
+\r
+ protected void makeGrpsFromSelection_actionPerformed()\r
+ {\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(\r
+ viewport.getSequenceSelection(),\r
+ viewport.getAlignmentView(true).getSequenceStrings(\r
+ viewport.getGapCharacter()),\r
+ viewport.alignment.getGroups());\r
+ viewport.alignment.deleteAllGroups();\r
+ viewport.sequenceColours = null;\r
+ viewport.setSelectionGroup(null);\r
+ // set view properties for each group\r
+ for (int g = 0; g < gps.length; g++)\r
+ {\r
+ // gps[g].setShowunconserved(viewport.getShowUnconserved());\r
+ gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());\r
+ viewport.alignment.addGroup(gps[g]);\r
+ Color col = new Color((int) (Math.random() * 255),\r
+ (int) (Math.random() * 255), (int) (Math.random() * 255));\r
+ col = col.brighter();\r
+ for (Enumeration sq = gps[g].getSequences(null).elements(); sq\r
+ .hasMoreElements(); viewport.setSequenceColour(\r
+ (SequenceI) sq.nextElement(), col))\r
+ ;\r
+ }\r
+ PaintRefresher.Refresh(this, viewport.getSequenceSetId());\r
+ alignPanel.updateAnnotation();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
}\r
\r
protected void deleteGroups_actionPerformed()\r
viewport.setSelectionGroup(sg);\r
alignPanel.paintAlignment(true);\r
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+ viewport.sendSelection();\r
}\r
\r
public void deselectAllSequenceMenuItem_actionPerformed()\r
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
alignPanel.paintAlignment(true);\r
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+ viewport.sendSelection();\r
}\r
\r
public void invertSequenceMenuItem_actionPerformed()\r
}\r
\r
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+ viewport.sendSelection();\r
+ }\r
+\r
+ public void invertColSel_actionPerformed()\r
+ {\r
+ viewport.invertColumnSelection();\r
+ alignPanel.paintAlignment(true);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
+ viewport.sendSelection();\r
}\r
\r
void trimAlignment(boolean trimLeft)\r
SequenceI[] seqs;\r
if (viewport.getSelectionGroup() != null)\r
{\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.\r
- hiddenRepSequences);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
+ viewport.hiddenRepSequences);\r
}\r
else\r
{\r
if (trimLeft)\r
{\r
trimRegion = new TrimRegionCommand("Remove Left",\r
- TrimRegionCommand.TRIM_LEFT,\r
- seqs,\r
- column,\r
- viewport.alignment,\r
- viewport.colSel,\r
- viewport.selectionGroup);\r
+ TrimRegionCommand.TRIM_LEFT, seqs, column,\r
+ viewport.alignment, viewport.colSel,\r
+ viewport.selectionGroup);\r
viewport.setStartRes(0);\r
}\r
else\r
{\r
trimRegion = new TrimRegionCommand("Remove Right",\r
- TrimRegionCommand.TRIM_RIGHT,\r
- seqs,\r
- column,\r
- viewport.alignment,\r
- viewport.colSel,\r
- viewport.selectionGroup);\r
+ TrimRegionCommand.TRIM_RIGHT, seqs, column,\r
+ viewport.alignment, viewport.colSel,\r
+ viewport.selectionGroup);\r
}\r
\r
statusBar.setText("Removed " + trimRegion.getSize() + " columns.");\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
\r
- if ( (trimLeft && !sg.adjustForRemoveLeft(column))\r
- || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
+ if ((trimLeft && !sg.adjustForRemoveLeft(column))\r
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
{\r
viewport.alignment.deleteGroup(sg);\r
}\r
}\r
\r
- viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\r
+ viewport.firePropertyChange("alignment", null, viewport\r
+ .getAlignment().getSequences());\r
}\r
}\r
\r
SequenceI[] seqs;\r
if (viewport.getSelectionGroup() != null)\r
{\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.\r
- hiddenRepSequences);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
+ viewport.hiddenRepSequences);\r
start = viewport.getSelectionGroup().getStartRes();\r
end = viewport.getSelectionGroup().getEndRes();\r
}\r
seqs = viewport.alignment.getSequencesArray();\r
}\r
\r
- RemoveGapColCommand removeGapCols =\r
- new RemoveGapColCommand("Remove Gapped Columns",\r
- seqs,\r
- start, end,\r
- viewport.alignment);\r
+ RemoveGapColCommand removeGapCols = new RemoveGapColCommand(\r
+ "Remove Gapped Columns", seqs, start, end, viewport.alignment);\r
\r
addHistoryItem(removeGapCols);\r
\r
- statusBar.setText("Removed " + removeGapCols.getSize() + " empty columns.");\r
+ statusBar.setText("Removed " + removeGapCols.getSize()\r
+ + " empty columns.");\r
\r
- //This is to maintain viewport position on first residue\r
- //of first sequence\r
+ // This is to maintain viewport position on first residue\r
+ // of first sequence\r
SequenceI seq = viewport.alignment.getSequenceAt(0);\r
int startRes = seq.findPosition(viewport.startRes);\r
// ShiftList shifts;\r
// viewport.getAlignment().removeGaps(shifts=new ShiftList());\r
// edit.alColumnChanges=shifts.getInverse();\r
// if (viewport.hasHiddenColumns)\r
- // viewport.getColumnSelection().compensateForEdits(shifts);\r
+ // viewport.getColumnSelection().compensateForEdits(shifts);\r
viewport.setStartRes(seq.findIndex(startRes) - 1);\r
- viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+ .getSequences());\r
\r
}\r
\r
SequenceI[] seqs;\r
if (viewport.getSelectionGroup() != null)\r
{\r
- seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.\r
- hiddenRepSequences);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(\r
+ viewport.hiddenRepSequences);\r
start = viewport.getSelectionGroup().getStartRes();\r
end = viewport.getSelectionGroup().getEndRes();\r
}\r
seqs = viewport.alignment.getSequencesArray();\r
}\r
\r
- //This is to maintain viewport position on first residue\r
- //of first sequence\r
+ // This is to maintain viewport position on first residue\r
+ // of first sequence\r
SequenceI seq = viewport.alignment.getSequenceAt(0);\r
int startRes = seq.findPosition(viewport.startRes);\r
\r
- addHistoryItem(new RemoveGapsCommand("Remove Gaps",\r
- seqs,\r
- start, end,\r
- viewport.alignment));\r
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,\r
+ viewport.alignment));\r
\r
viewport.setStartRes(seq.findIndex(startRes) - 1);\r
\r
- viewport.firePropertyChange("alignment", null,\r
- viewport.getAlignment().getSequences());\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment()\r
+ .getSequences());\r
\r
}\r
\r
new Finder(alignPanel);\r
}\r
\r
- public void newView()\r
+ /**\r
+ * create a new view derived from the current view\r
+ * \r
+ * @param viewtitle\r
+ * @return frame for the new view\r
+ */\r
+ public AlignFrame newView(String viewtitle)\r
{\r
AlignmentI newal;\r
if (viewport.hasHiddenRows)\r
{\r
- newal = new Alignment(viewport.getAlignment().\r
- getHiddenSequences()\r
- .getFullAlignment().\r
- getSequencesArray());\r
+ newal = new Alignment(viewport.getAlignment().getHiddenSequences()\r
+ .getFullAlignment().getSequencesArray());\r
}\r
else\r
{\r
}\r
}\r
\r
- AlignFrame newaf = new AlignFrame(newal,\r
- viewport.applet,\r
- "",\r
- false);\r
+ AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);\r
\r
newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();\r
PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
PaintRefresher.Register(newaf.alignPanel,\r
- newaf.alignPanel.av.getSequenceSetId());\r
+ newaf.alignPanel.av.getSequenceSetId());\r
\r
PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,\r
- newaf.alignPanel.av.getSequenceSetId());\r
+ newaf.alignPanel.av.getSequenceSetId());\r
PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
- newaf.alignPanel.av.getSequenceSetId());\r
+ newaf.alignPanel.av.getSequenceSetId());\r
\r
- Vector comps = (Vector) PaintRefresher.components.get(viewport.\r
- getSequenceSetId());\r
+ Vector comps = (Vector) PaintRefresher.components.get(viewport\r
+ .getSequenceSetId());\r
int viewSize = -1;\r
for (int i = 0; i < comps.size(); i++)\r
{\r
}\r
\r
String title = new String(this.getTitle());\r
- if (title.indexOf("(View") > -1)\r
+ if (viewtitle != null)\r
{\r
- title = title.substring(0, title.indexOf("(View"));\r
+ title = viewtitle + " ( " + title + ")";\r
+ }\r
+ else\r
+ {\r
+ if (title.indexOf("(View") > -1)\r
+ {\r
+ title = title.substring(0, title.indexOf("(View"));\r
+ }\r
+ title += "(View " + viewSize + ")";\r
}\r
-\r
- title += "(View " + viewSize + ")";\r
\r
newaf.setTitle(title.toString());\r
\r
newaf.viewport.historyList = viewport.historyList;\r
newaf.viewport.redoList = viewport.redoList;\r
+ return newaf;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return list of feature groups on the view\r
+ */\r
+ public String[] getFeatureGroups()\r
+ {\r
+ FeatureRenderer fr = null;\r
+ if (alignPanel != null\r
+ && (fr = alignPanel.getFeatureRenderer()) != null)\r
+ {\r
+ return fr.getGroups();\r
+ }\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * get sequence feature groups that are hidden or shown\r
+ * \r
+ * @param visible\r
+ * true is visible\r
+ * @return list\r
+ */\r
+ public String[] getFeatureGroupsOfState(boolean visible)\r
+ {\r
+ FeatureRenderer fr = null;\r
+ if (alignPanel != null\r
+ && (fr = alignPanel.getFeatureRenderer()) != null)\r
+ {\r
+ return fr.getGroups(visible);\r
+ }\r
+ return null;\r
+ }\r
\r
+ /**\r
+ * Change the display state for the given feature groups\r
+ * \r
+ * @param groups\r
+ * list of group strings\r
+ * @param state\r
+ * visible or invisible\r
+ */\r
+ public void setFeatureGroupState(String[] groups, boolean state)\r
+ {\r
+ FeatureRenderer fr = null;\r
+ this.sequenceFeatures.setState(true);\r
+ viewport.showSequenceFeatures(true);\r
+ if (alignPanel != null\r
+ && (fr = alignPanel.getFeatureRenderer()) != null)\r
+ {\r
+ fr.setGroupState(groups, state);\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ if (alignPanel.overviewPanel != null)\r
+ {\r
+ alignPanel.overviewPanel.updateOverviewImage();\r
+ }\r
+ }\r
}\r
\r
public void seqLimits_itemStateChanged()\r
alignPanel.paintAlignment(true);\r
}\r
\r
+ protected void displayNonconservedMenuItem_actionPerformed()\r
+ {\r
+ viewport.setShowunconserved(displayNonconservedMenuItem.getState());\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
protected void wrapMenuItem_actionPerformed()\r
{\r
viewport.setWrapAlignment(wrapMenuItem.getState());\r
frame.add(overview);\r
// +50 must allow for applet frame window\r
jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
- overview.getPreferredSize().width,\r
- overview.getPreferredSize().height + 50);\r
+ overview.getPreferredSize().width,\r
+ overview.getPreferredSize().height + 50);\r
\r
frame.pack();\r
frame.addWindowListener(new WindowAdapter()\r
{\r
if (viewport.getAbovePIDThreshold())\r
{\r
- threshold = SliderPanel.setPIDSliderSource(alignPanel, cs, "Background");\r
+ threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,\r
+ "Background");\r
\r
cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
\r
\r
Alignment al = (Alignment) viewport.alignment;\r
Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- al.getSequences(), 0,\r
- al.getWidth() - 1);\r
+ ResidueProperties.propHash, 3, al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
\r
cs.setConservation(c);\r
\r
- cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel, cs,\r
- "Background"));\r
+ cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,\r
+ cs, "Background"));\r
\r
}\r
else\r
if (cs instanceof ClustalxColourScheme)\r
{\r
sg.cs = new ClustalxColourScheme(\r
- sg.getSequences(viewport.hiddenRepSequences),\r
- sg.getWidth());\r
+ sg.getSequences(viewport.hiddenRepSequences),\r
+ sg.getWidth());\r
}\r
else\r
{\r
try\r
{\r
sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
- }\r
- catch (Exception ex)\r
+ } catch (Exception ex)\r
{\r
ex.printStackTrace();\r
sg.cs = cs;\r
}\r
\r
if (viewport.getAbovePIDThreshold()\r
- || cs instanceof PIDColourScheme\r
- || cs instanceof Blosum62ColourScheme)\r
+ || cs instanceof PIDColourScheme\r
+ || cs instanceof Blosum62ColourScheme)\r
{\r
sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));\r
+ sg.getSequences(viewport.hiddenRepSequences), 0,\r
+ sg.getWidth()));\r
}\r
else\r
{\r
if (viewport.getConservationSelected())\r
{\r
Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.getSequences(viewport.\r
- hiddenRepSequences), 0,\r
- viewport.alignment.getWidth() - 1);\r
+ ResidueProperties.propHash, 3,\r
+ sg.getSequences(viewport.hiddenRepSequences), 0,\r
+ viewport.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
sg.cs.setConservation(c);\r
alignPanel.getOverviewPanel().updateOverviewImage();\r
}\r
\r
- jalview.structure.StructureSelectionManager.getStructureSelectionManager()\r
- .sequenceColoursChanged(alignPanel);\r
+ jalview.structure.StructureSelectionManager\r
+ .getStructureSelectionManager(viewport.applet).sequenceColoursChanged(\r
+ alignPanel);\r
\r
alignPanel.paintAlignment(true);\r
}\r
\r
protected void modifyPID_actionPerformed()\r
{\r
- if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null)\r
+ if (viewport.getAbovePIDThreshold()\r
+ && viewport.globalColourScheme != null)\r
{\r
- SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
- "Background");\r
+ SliderPanel.setPIDSliderSource(alignPanel,\r
+ viewport.getGlobalColourScheme(), "Background");\r
SliderPanel.showPIDSlider();\r
}\r
}\r
\r
protected void modifyConservation_actionPerformed()\r
{\r
- if (viewport.getConservationSelected() && viewport.globalColourScheme != null)\r
+ if (viewport.getConservationSelected()\r
+ && viewport.globalColourScheme != null)\r
{\r
- SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
- "Background");\r
+ SliderPanel.setConservationSlider(alignPanel,\r
+ viewport.globalColourScheme, "Background");\r
SliderPanel.showConservationSlider();\r
}\r
}\r
public void sortPairwiseMenuItem_actionPerformed()\r
{\r
SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
- AlignmentSorter.sortByPID(viewport.getAlignment(),\r
- viewport.getAlignment().getSequenceAt(0));\r
+ AlignmentSorter.sortByPID(viewport.getAlignment(), viewport\r
+ .getAlignment().getSequenceAt(0), null);\r
+\r
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,\r
- viewport.alignment));\r
+ viewport.alignment));\r
alignPanel.paintAlignment(true);\r
}\r
\r
public void sortIDMenuItem_actionPerformed()\r
{\r
- // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
- // HistoryItem.SORT));\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
AlignmentSorter.sortByID(viewport.getAlignment());\r
+ addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment));\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public void sortLengthMenuItem_actionPerformed()\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter.sortByLength(viewport.getAlignment());\r
+ addHistoryItem(new OrderCommand("Length Sort", oldOrder,\r
+ viewport.alignment));\r
alignPanel.paintAlignment(true);\r
}\r
\r
public void sortGroupMenuItem_actionPerformed()\r
{\r
- // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
- // HistoryItem.SORT));\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
AlignmentSorter.sortByGroup(viewport.getAlignment());\r
+ addHistoryItem(new OrderCommand("Group Sort", oldOrder,\r
+ viewport.alignment));\r
alignPanel.paintAlignment(true);\r
\r
}\r
public void pairwiseAlignmentMenuItem_actionPerformed()\r
{\r
if (viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().getSize() > 1)\r
+ && viewport.getSelectionGroup().getSize() > 1)\r
{\r
Frame frame = new Frame();\r
frame.add(new PairwiseAlignPanel(alignPanel));\r
- jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,\r
+ 500);\r
}\r
}\r
\r
public void PCAMenuItem_actionPerformed()\r
{\r
- //are the sequences aligned?\r
- if (!viewport.alignment.isAligned())\r
+ // are the sequences aligned?\r
+ if (!viewport.alignment.isAligned(false))\r
{\r
SequenceI current;\r
int Width = viewport.getAlignment().getWidth();\r
\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
- i++)\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
{\r
current = viewport.getAlignment().getSequenceAt(i);\r
\r
alignPanel.paintAlignment(true);\r
}\r
\r
- if ( (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize() < 4 &&\r
- viewport.getSelectionGroup().getSize() > 0)\r
- || viewport.getAlignment().getHeight() < 4)\r
+ if ((viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().getSize() < 4 && viewport\r
+ .getSelectionGroup().getSize() > 0)\r
+ || viewport.getAlignment().getHeight() < 4)\r
{\r
return;\r
}\r
try\r
{\r
new PCAPanel(viewport);\r
- }\r
- catch (java.lang.OutOfMemoryError ex)\r
+ } catch (java.lang.OutOfMemoryError ex)\r
{\r
}\r
\r
\r
void NewTreePanel(String type, String pwType, String title)\r
{\r
- //are the sequences aligned?\r
- if (!viewport.alignment.isAligned())\r
+ // are the sequences aligned?\r
+ if (!viewport.alignment.isAligned(false))\r
{\r
SequenceI current;\r
int Width = viewport.getAlignment().getWidth();\r
\r
- for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
- i++)\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
{\r
current = viewport.getAlignment().getSequenceAt(i);\r
\r
\r
}\r
\r
- if ( (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize() > 1)\r
- || (viewport.getSelectionGroup() == null\r
- && viewport.alignment.getHeight() > 1))\r
+ if ((viewport.getSelectionGroup() != null && viewport\r
+ .getSelectionGroup().getSize() > 1)\r
+ || (viewport.getSelectionGroup() == null && viewport.alignment\r
+ .getHeight() > 1))\r
{\r
- final TreePanel tp = new TreePanel(viewport,\r
- type,\r
- pwType);\r
+ final TreePanel tp = new TreePanel(alignPanel, type, pwType);\r
\r
addTreeMenuItem(tp, title);\r
\r
\r
public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
{\r
- TreePanel tp = new TreePanel(viewport,\r
- treeFile,\r
- "From File - ",\r
- tree);\r
+ TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);\r
jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
addTreeMenuItem(tp, treeFile);\r
}\r
\r
- void addTreeMenuItem(final TreePanel treePanel, String title)\r
+ /**\r
+ * sort the alignment using the given treePanel\r
+ * \r
+ * @param treePanel\r
+ * tree used to sort view\r
+ * @param title\r
+ * string used for undo event name\r
+ */\r
+ public void sortByTree(TreePanel treePanel, String title)\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
+ AlignmentSorter\r
+ .sortByTree(viewport.getAlignment(), treePanel.getTree());\r
+ // addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
+ // HistoryItem.SORT));\r
+ addHistoryItem(new OrderCommand("Order by " + title, oldOrder,\r
+ viewport.alignment));\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * Do any automatic reordering of the alignment and add the necessary bits to\r
+ * the menu structure for the new tree\r
+ * \r
+ * @param treePanel\r
+ * @param title\r
+ */\r
+ protected void addTreeMenuItem(final TreePanel treePanel,\r
+ final String title)\r
{\r
final MenuItem item = new MenuItem(title);\r
sortByTreeMenu.add(item);\r
{\r
public void actionPerformed(ActionEvent evt)\r
{\r
- // addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
- // HistoryItem.SORT));\r
- AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
- alignPanel.paintAlignment(true);\r
+ sortByTree(treePanel, title); // treePanel.getTitle());\r
}\r
});\r
-\r
+ \r
treePanel.addWindowListener(new WindowAdapter()\r
{\r
+ public void windowOpened(WindowEvent e)\r
+ {\r
+ if (viewport.sortByTree)\r
+ {\r
+ sortByTree(treePanel, title);\r
+ }\r
+ super.windowOpened(e);\r
+ }\r
+\r
public void windowClosing(WindowEvent e)\r
{\r
sortByTreeMenu.remove(item);\r
};\r
});\r
}\r
+ public boolean sortBy(AlignmentOrder alorder, String undoname)\r
+ {\r
+ SequenceI[] oldOrder = viewport.getAlignment()\r
+ .getSequencesArray();\r
+ if (viewport.applet.debug)\r
+ {\r
+ System.err.println("Sorting "+alorder.getOrder().size()+" in alignment '"+getTitle()+"'");\r
+ }\r
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);\r
+ if (undoname!=null)\r
+ {\r
+ addHistoryItem(new OrderCommand(undoname, oldOrder, viewport.alignment));\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ return true;\r
+ }\r
\r
protected void documentation_actionPerformed()\r
{\r
- showURL("http://www.jalview.org/help.html", "HELP");\r
+ alignPanel.av.applet.openJalviewHelpUrl();\r
}\r
\r
protected void about_actionPerformed()\r
{\r
\r
- class AboutPanel\r
- extends Canvas\r
+ class AboutPanel extends Canvas\r
{\r
String version;\r
- public AboutPanel(String version)\r
+\r
+ String builddate;\r
+\r
+ public AboutPanel(String version, String builddate)\r
{\r
this.version = version;\r
+ this.builddate = builddate;\r
}\r
\r
public void paint(Graphics g)\r
int fh = fm.getHeight();\r
int y = 5, x = 7;\r
g.setColor(Color.black);\r
+ // TODO: update this text for each release or centrally store it for\r
+ // lite and application\r
g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
- g.drawString("Jalview - Release " + version, 200, y += fh);\r
+ g.drawString("JalviewLite - Release " + version, x, y += fh);\r
+ g.setFont(new Font("Helvetica", Font.BOLD, 12));\r
+ g.drawString("Build date: " + builddate, x, y += fh);\r
g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
- g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
- x, y += fh * 2);\r
- g.drawString("Current development managed by Andrew Waterhouse; Barton Group, University of Dundee.",\r
- x, y += fh);\r
g.drawString(\r
- "For any issues relating to Jalview, email help@jalview.org", x,\r
- y += fh);\r
- g.drawString("If you use JalView, please cite:", x, y += fh + 8);\r
- g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
- x, y += fh);\r
- g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);\r
- }\r
- }\r
-\r
- String version = "test";\r
- java.net.URL url = getClass().getResource("/.build_properties");\r
- if (url != null)\r
- {\r
- try\r
- {\r
- BufferedReader reader = new BufferedReader(new InputStreamReader(\r
- url.openStream()));\r
- String line;\r
- while ( (line = reader.readLine()) != null)\r
- {\r
- if (line.indexOf("VERSION") > -1)\r
- {\r
- version = line.substring(line.indexOf("=") + 1);\r
- }\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
+ "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",\r
+ x, y += fh * 1.5);\r
+ g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);\r
+ g.drawString(\r
+ "Development managed by The Barton Group, University of Dundee, Scotland, UK.",\r
+ x, y += fh);\r
+ g.drawString(\r
+ "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",\r
+ x, y += fh);\r
+ g.drawString("If you use Jalview, please cite:", x, y += fh + 8);\r
+ g.drawString(\r
+ "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",\r
+ x, y += fh);\r
+ g.drawString(\r
+ "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",\r
+ x, y += fh);\r
+ g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",\r
+ x, y += fh);\r
}\r
}\r
\r
Frame frame = new Frame();\r
- frame.add(new AboutPanel(version));\r
- jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
+ frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite\r
+ .getBuildDate()));\r
+ jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);\r
\r
}\r
\r
}\r
else\r
{\r
- try\r
- {\r
- System.out.println("Show url: " + url);\r
- viewport.applet.getAppletContext().showDocument(new java.net.URL(url),\r
- target);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\r
- //////////////////////////////////////////////////////////////////////////////////\r
- //JBuilder Graphics here\r
-\r
- MenuBar alignFrameMenuBar = new MenuBar();\r
- Menu fileMenu = new Menu("File");\r
- MenuItem loadApplication = new MenuItem("View in Full Application");\r
- MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
- MenuItem loadAnnotations = new MenuItem(\r
- "Load Features/Annotations ...");\r
- MenuItem outputFeatures = new MenuItem("Export Features ...");\r
- MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
-\r
- MenuItem closeMenuItem = new MenuItem("Close");\r
- Menu editMenu = new Menu("Edit");\r
- Menu viewMenu = new Menu("View");\r
- Menu colourMenu = new Menu("Colour");\r
- Menu calculateMenu = new Menu("Calculate");\r
- MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
- MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
- MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
- MenuItem remove2LeftMenuItem = new MenuItem();\r
- MenuItem remove2RightMenuItem = new MenuItem();\r
- MenuItem removeGappedColumnMenuItem = new MenuItem();\r
- MenuItem removeAllGapsMenuItem = new MenuItem();\r
- CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
- CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
- MenuItem sortPairwiseMenuItem = new MenuItem();\r
- MenuItem sortIDMenuItem = new MenuItem();\r
- MenuItem sortGroupMenuItem = new MenuItem();\r
- MenuItem removeRedundancyMenuItem = new MenuItem();\r
- MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
- MenuItem PCAMenuItem = new MenuItem();\r
- MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
- MenuItem neighbourTreeMenuItem = new MenuItem();\r
+ viewport.applet.showURL(url, target);\r
+ }\r
+ }\r
+\r
+ // ////////////////////////////////////////////////////////////////////////////////\r
+ // JBuilder Graphics here\r
+\r
+ MenuBar alignFrameMenuBar = new MenuBar();\r
+\r
+ Menu fileMenu = new Menu("File");\r
+\r
+ MenuItem loadApplication = new MenuItem("View in Full Application");\r
+\r
+ MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
+\r
+ MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
+\r
+ MenuItem outputFeatures = new MenuItem("Export Features ...");\r
+\r
+ MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
+\r
+ MenuItem closeMenuItem = new MenuItem("Close");\r
+\r
+ Menu editMenu = new Menu("Edit");\r
+\r
+ Menu viewMenu = new Menu("View");\r
+\r
+ Menu colourMenu = new Menu("Colour");\r
+\r
+ Menu calculateMenu = new Menu("Calculate");\r
+\r
+ MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
+\r
+ MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
+\r
+ MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
+\r
+ MenuItem remove2LeftMenuItem = new MenuItem();\r
+\r
+ MenuItem remove2RightMenuItem = new MenuItem();\r
+\r
+ MenuItem removeGappedColumnMenuItem = new MenuItem();\r
+\r
+ MenuItem removeAllGapsMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem sortPairwiseMenuItem = new MenuItem();\r
+\r
+ MenuItem sortIDMenuItem = new MenuItem();\r
+\r
+ MenuItem sortLengthMenuItem = new MenuItem();\r
+\r
+ MenuItem sortGroupMenuItem = new MenuItem();\r
+\r
+ MenuItem removeRedundancyMenuItem = new MenuItem();\r
+\r
+ MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
+\r
+ MenuItem PCAMenuItem = new MenuItem();\r
+\r
+ MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
+\r
+ MenuItem neighbourTreeMenuItem = new MenuItem();\r
+\r
BorderLayout borderLayout1 = new BorderLayout();\r
+\r
public Label statusBar = new Label();\r
- Menu outputTextboxMenu = new Menu();\r
- MenuItem clustalColour = new MenuItem();\r
- MenuItem zappoColour = new MenuItem();\r
- MenuItem taylorColour = new MenuItem();\r
- MenuItem hydrophobicityColour = new MenuItem();\r
- MenuItem helixColour = new MenuItem();\r
- MenuItem strandColour = new MenuItem();\r
- MenuItem turnColour = new MenuItem();\r
- MenuItem buriedColour = new MenuItem();\r
- MenuItem userDefinedColour = new MenuItem();\r
- MenuItem PIDColour = new MenuItem();\r
- MenuItem BLOSUM62Colour = new MenuItem();\r
+\r
+ Menu outputTextboxMenu = new Menu();\r
+\r
+ MenuItem clustalColour = new MenuItem();\r
+\r
+ MenuItem zappoColour = new MenuItem();\r
+\r
+ MenuItem taylorColour = new MenuItem();\r
+\r
+ MenuItem hydrophobicityColour = new MenuItem();\r
+\r
+ MenuItem helixColour = new MenuItem();\r
+\r
+ MenuItem strandColour = new MenuItem();\r
+\r
+ MenuItem turnColour = new MenuItem();\r
+\r
+ MenuItem buriedColour = new MenuItem();\r
+\r
+ MenuItem userDefinedColour = new MenuItem();\r
+\r
+ MenuItem PIDColour = new MenuItem();\r
+\r
+ MenuItem BLOSUM62Colour = new MenuItem();\r
+\r
MenuItem njTreeBlosumMenuItem = new MenuItem();\r
+\r
MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
- CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
- CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
- MenuItem alProperties = new MenuItem("Alignment Properties...");\r
+\r
+ CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem alProperties = new MenuItem("Alignment Properties...");\r
+\r
MenuItem overviewMenuItem = new MenuItem();\r
- MenuItem undoMenuItem = new MenuItem();\r
- MenuItem redoMenuItem = new MenuItem();\r
- CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem undoMenuItem = new MenuItem();\r
+\r
+ MenuItem redoMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
+\r
MenuItem noColourmenuItem = new MenuItem();\r
- CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
- CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
+\r
MenuItem findMenuItem = new MenuItem();\r
- CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
- MenuItem nucleotideColour = new MenuItem();\r
+\r
+ CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
+\r
+ MenuItem nucleotideColour = new MenuItem();\r
+\r
MenuItem deleteGroups = new MenuItem();\r
+\r
+ MenuItem grpsFromSelection = new MenuItem();\r
+\r
MenuItem delete = new MenuItem();\r
+\r
MenuItem copy = new MenuItem();\r
+\r
MenuItem cut = new MenuItem();\r
+\r
Menu pasteMenu = new Menu();\r
+\r
MenuItem pasteNew = new MenuItem();\r
+\r
MenuItem pasteThis = new MenuItem();\r
- CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
- MenuItem font = new MenuItem();\r
- CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
- CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
- CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
+\r
+ MenuItem font = new MenuItem();\r
+\r
+ CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
+\r
MenuItem modifyPID = new MenuItem();\r
+\r
MenuItem modifyConservation = new MenuItem();\r
- CheckboxMenuItem autoCalculate\r
- = new CheckboxMenuItem("Autocalculate Consensus", true);\r
- Menu sortByTreeMenu = new Menu();\r
+\r
+ CheckboxMenuItem autoCalculate = new CheckboxMenuItem(\r
+ "Autocalculate Consensus", true);\r
+\r
+ CheckboxMenuItem sortByTree = new CheckboxMenuItem(\r
+ "Sort Alignment With New Tree", true);\r
+\r
+ Menu sortByTreeMenu = new Menu();\r
+\r
Menu sort = new Menu();\r
+\r
Menu calculate = new Menu();\r
+\r
MenuItem inputText = new MenuItem();\r
+\r
Menu helpMenu = new Menu();\r
+\r
MenuItem documentation = new MenuItem();\r
+\r
MenuItem about = new MenuItem();\r
- CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
- Panel embeddedMenu;\r
- Label embeddedEdit;\r
- Label embeddedSelect;\r
- Label embeddedView;\r
- Label embeddedFormat;\r
- Label embeddedColour;\r
- Label embeddedFile;\r
- Label embeddedHelp;\r
- Label embeddedCalculate;\r
- FlowLayout flowLayout1;\r
-\r
- private void jbInit()\r
- throws Exception\r
+\r
+ CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();\r
+ \r
+ CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();\r
+ Menu autoAnnMenu=new Menu();\r
+ CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();\r
+ CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();\r
+ CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();\r
+ CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();\r
+ CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();\r
+\r
+ private void jbInit() throws Exception\r
{\r
\r
setMenuBar(alignFrameMenuBar);\r
MenuItem item;\r
\r
// dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;\r
- i++)\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
{\r
\r
- item = new MenuItem(jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
+ item = new MenuItem(\r
+ jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
sortPairwiseMenuItem.addActionListener(this);\r
sortIDMenuItem.setLabel("by ID");\r
sortIDMenuItem.addActionListener(this);\r
+ sortLengthMenuItem.setLabel("by Length");\r
+ sortLengthMenuItem.addActionListener(this);\r
sortGroupMenuItem.setLabel("by Group");\r
sortGroupMenuItem.addActionListener(this);\r
removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
pairwiseAlignmentMenuItem.addActionListener(this);\r
PCAMenuItem.setLabel("Principal Component Analysis");\r
PCAMenuItem.addActionListener(this);\r
- averageDistanceTreeMenuItem.setLabel(\r
- "Average Distance Using % Identity");\r
+ averageDistanceTreeMenuItem\r
+ .setLabel("Average Distance Using % Identity");\r
averageDistanceTreeMenuItem.addActionListener(this);\r
neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
neighbourTreeMenuItem.addActionListener(this);\r
PIDColour.addActionListener(this);\r
BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
BLOSUM62Colour.addActionListener(this);\r
- avDistanceTreeBlosumMenuItem.setLabel(\r
- "Average Distance Using BLOSUM62");\r
+ avDistanceTreeBlosumMenuItem\r
+ .setLabel("Average Distance Using BLOSUM62");\r
avDistanceTreeBlosumMenuItem.addActionListener(this);\r
njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
njTreeBlosumMenuItem.addActionListener(this);\r
annotationPanelMenuItem.addItemListener(this);\r
colourTextMenuItem.setLabel("Colour Text");\r
colourTextMenuItem.addItemListener(this);\r
+ displayNonconservedMenuItem.setLabel("Show nonconserved");\r
+ displayNonconservedMenuItem.addItemListener(this);\r
alProperties.addActionListener(this);\r
overviewMenuItem.setLabel("Overview Window");\r
overviewMenuItem.addActionListener(this);\r
nucleotideColour.addActionListener(this);\r
deleteGroups.setLabel("Undefine Groups");\r
deleteGroups.addActionListener(this);\r
+ grpsFromSelection.setLabel("Make Groups for selection");\r
+ grpsFromSelection.addActionListener(this);\r
copy.setLabel("Copy");\r
copy.addActionListener(this);\r
cut.setLabel("Cut");\r
sort.setLabel("Sort");\r
calculate.setLabel("Calculate Tree");\r
autoCalculate.addItemListener(this);\r
+ sortByTree.addItemListener(this);\r
inputText.setLabel("Input from textbox");\r
inputText.addActionListener(this);\r
-\r
+ centreColumnLabelFlag.setLabel("Centre column labels");\r
+ centreColumnLabelFlag.addItemListener(this);\r
+ followMouseOverFlag.setLabel("Automatic Scrolling");\r
+ followMouseOverFlag.addItemListener(this);\r
helpMenu.setLabel("Help");\r
documentation.setLabel("Documentation");\r
documentation.addActionListener(this);\r
menu2.setLabel("Hide");\r
hideColumns.setLabel("Selected Columns");\r
hideSequences.setLabel("Selected Sequences");\r
+ hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");\r
+ hideAllSelection.setLabel("Selected Region");\r
+ showAllHidden.setLabel("All Sequences and Columns");\r
+ showGroupConsensus.setLabel("Group Consensus");\r
+ showGroupConservation.setLabel("Group Conservation");\r
+ showConsensusHistogram.setLabel("Show Consensus Histogram");\r
+ showSequenceLogo.setLabel("Show Consensus Logo");\r
+ applyAutoAnnotationSettings.setLabel("Apply to all groups");\r
+ applyAutoAnnotationSettings.setState(true);\r
+ autoAnnMenu.setLabel("Autocalculated Annotation");\r
+ \r
invertColSel.addActionListener(this);\r
showColumns.addActionListener(this);\r
showSeqs.addActionListener(this);\r
hideColumns.addActionListener(this);\r
hideSequences.addActionListener(this);\r
+ hideAllButSelection.addActionListener(this);\r
+ hideAllSelection.addActionListener(this);\r
+ showAllHidden.addActionListener(this);\r
+ showGroupConsensus.addItemListener(this);\r
+ showGroupConservation.addItemListener(this);\r
+ showConsensusHistogram.addItemListener(this);\r
+ showSequenceLogo.addItemListener(this);\r
+ applyAutoAnnotationSettings.addItemListener(this);\r
formatMenu.setLabel("Format");\r
selectMenu.setLabel("Select");\r
newView.setLabel("New View");\r
viewMenu.add(menu1);\r
viewMenu.add(menu2);\r
viewMenu.addSeparator();\r
+ viewMenu.add(followMouseOverFlag);\r
viewMenu.add(annotationPanelMenuItem);\r
+ autoAnnMenu.add(applyAutoAnnotationSettings);\r
+ autoAnnMenu.add(showConsensusHistogram);\r
+ autoAnnMenu.add(showSequenceLogo);\r
+ autoAnnMenu.addSeparator();\r
+ autoAnnMenu.add(showGroupConservation);\r
+ autoAnnMenu.add(showGroupConsensus);\r
+ viewMenu.add(autoAnnMenu);\r
viewMenu.addSeparator();\r
viewMenu.add(sequenceFeatures);\r
viewMenu.add(featureSettings);\r
calculateMenu.add(pairwiseAlignmentMenuItem);\r
calculateMenu.add(PCAMenuItem);\r
calculateMenu.add(autoCalculate);\r
+ calculateMenu.add(sortByTree);\r
this.add(statusBar, BorderLayout.SOUTH);\r
pasteMenu.add(pasteNew);\r
pasteMenu.add(pasteThis);\r
sort.add(sortIDMenuItem);\r
+ sort.add(sortLengthMenuItem);\r
sort.add(sortByTreeMenu);\r
sort.add(sortGroupMenuItem);\r
sort.add(sortPairwiseMenuItem);\r
helpMenu.add(about);\r
menu1.add(showColumns);\r
menu1.add(showSeqs);\r
+ menu1.add(showAllHidden);\r
menu2.add(hideColumns);\r
menu2.add(hideSequences);\r
+ menu2.add(hideAllSelection);\r
+ menu2.add(hideAllButSelection);\r
formatMenu.add(font);\r
formatMenu.add(seqLimits);\r
formatMenu.add(wrapMenuItem);\r
formatMenu.add(viewBoxesMenuItem);\r
formatMenu.add(viewTextMenuItem);\r
formatMenu.add(colourTextMenuItem);\r
+ formatMenu.add(displayNonconservedMenuItem);\r
formatMenu.add(renderGapsMenuItem);\r
+ formatMenu.add(centreColumnLabelFlag);\r
selectMenu.add(findMenuItem);\r
selectMenu.addSeparator();\r
selectMenu.add(selectAllSequenceMenuItem);\r
selectMenu.add(deselectAllSequenceMenuItem);\r
selectMenu.add(invertSequenceMenuItem);\r
selectMenu.add(invertColSel);\r
+ selectMenu.add(grpsFromSelection);\r
selectMenu.add(deleteGroups);\r
+\r
}\r
\r
- public void setEmbedded()\r
- {\r
-\r
- embeddedMenu = new Panel();\r
- embeddedEdit = new Label("Edit");\r
- embeddedSelect = new Label("Select");\r
- embeddedView = new Label("View");\r
- embeddedFormat = new Label("Format");\r
- embeddedColour = new Label("Colour");\r
- embeddedFile = new Label("File");\r
- embeddedHelp = new Label("Help");\r
- embeddedCalculate = new Label("Calculate");\r
- flowLayout1 = new FlowLayout();\r
- embeddedMenu.setBackground(Color.lightGray);\r
- embeddedMenu.setLayout(flowLayout1);\r
- embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
- embeddedMenu.add(embeddedFile);\r
- embeddedMenu.add(embeddedEdit);\r
- embeddedMenu.add(embeddedSelect);\r
- embeddedMenu.add(embeddedView);\r
- embeddedMenu.add(embeddedFormat);\r
- embeddedMenu.add(embeddedColour);\r
- embeddedMenu.add(embeddedCalculate);\r
- embeddedMenu.add(embeddedHelp);\r
- flowLayout1.setAlignment(FlowLayout.LEFT);\r
- flowLayout1.setHgap(2);\r
- flowLayout1.setVgap(0);\r
- embeddedFile.addMouseListener(this);\r
- embeddedEdit.addMouseListener(this);\r
- embeddedSelect.addMouseListener(this);\r
- embeddedView.addMouseListener(this);\r
- embeddedFormat.addMouseListener(this);\r
- embeddedColour.addMouseListener(this);\r
- embeddedCalculate.addMouseListener(this);\r
- embeddedHelp.addMouseListener(this);\r
-\r
- fileMenu.remove(closeMenuItem);\r
- fileMenu.remove(3); // Seperator\r
-\r
- viewport.applet.setLayout(new BorderLayout());\r
- viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
- viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
-\r
- alignPanel.setSize(viewport.applet.getSize().width,\r
- viewport.applet.getSize().height\r
- - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
-\r
- viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
- viewport.applet.validate();\r
-\r
- }\r
-\r
- PopupMenu filePopup, editPopup, searchPopup,\r
- viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;\r
MenuItem featureSettings = new MenuItem();\r
+\r
CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
+\r
MenuItem annotationColour = new MenuItem();\r
+\r
MenuItem invertColSel = new MenuItem();\r
+\r
Menu menu1 = new Menu();\r
+\r
MenuItem showColumns = new MenuItem();\r
+\r
MenuItem showSeqs = new MenuItem();\r
+\r
Menu menu2 = new Menu();\r
+\r
MenuItem hideColumns = new MenuItem();\r
+\r
MenuItem hideSequences = new MenuItem();\r
+\r
+ MenuItem hideAllButSelection = new MenuItem();\r
+\r
+ MenuItem hideAllSelection = new MenuItem();\r
+\r
+ MenuItem showAllHidden = new MenuItem();\r
+\r
Menu formatMenu = new Menu();\r
+\r
Menu selectMenu = new Menu();\r
+\r
MenuItem newView = new MenuItem();\r
\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- PopupMenu popup = null;\r
- Label source = (Label) evt.getSource();\r
- if (source == embeddedFile)\r
- {\r
- popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
+ /**\r
+ * Attach the alignFrame panels after embedding menus, if necessary. This used\r
+ * to be called setEmbedded, but is now creates the dropdown menus in a\r
+ * platform independent manner to avoid OSX/Mac menu appendage daftness.\r
+ * \r
+ * @param reallyEmbedded\r
+ * true to attach the view to the applet area on the page rather than\r
+ * in a new window\r
+ */\r
+ public void createAlignFrameWindow(boolean reallyEmbedded, String title)\r
+ {\r
+ if (reallyEmbedded)\r
+ {\r
+ // ////\r
+ // Explicly build the embedded menu panel for the on-page applet\r
+ //\r
+ // view cannot be closed if its actually on the page\r
+ fileMenu.remove(closeMenuItem);\r
+ fileMenu.remove(3); // Remove Seperator\r
+ embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",\r
+ Font.PLAIN, 10, false); // use our own fonts.\r
+ // and actually add the components to the applet area\r
+ viewport.applet.setLayout(new BorderLayout());\r
+ viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
+ viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
+ alignPanel.setSize(viewport.applet.getSize().width,\r
+ viewport.applet.getSize().height - embeddedMenu.HEIGHT\r
+ - statusBar.HEIGHT);\r
+ viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
+ final AlignFrame me = this;\r
+ viewport.applet.addFocusListener(new FocusListener()\r
+ {\r
+ \r
+ @Override\r
+ public void focusLost(FocusEvent e)\r
+ {\r
+ if (me.viewport.applet.currentAlignFrame==me) {\r
+ me.viewport.applet.currentAlignFrame = null;\r
+ }}\r
+ \r
+ @Override\r
+ public void focusGained(FocusEvent e)\r
+ {\r
+ me.viewport.applet.currentAlignFrame = me;\r
+ }\r
+ });\r
+ viewport.applet.validate();\r
}\r
- else if (source == embeddedEdit)\r
+ else\r
{\r
- popup = editPopup = genPopupMenu(editPopup, editMenu);\r
+ // //////\r
+ // test and embed menu bar if necessary.\r
+ //\r
+ if (embedMenuIfNeeded(alignPanel))\r
+ {\r
+ // adjust for status bar height too\r
+ alignPanel.setSize(getSize().width, getSize().height\r
+ - statusBar.HEIGHT);\r
+ }\r
+ add(statusBar, BorderLayout.SOUTH);\r
+ add(alignPanel, BorderLayout.CENTER);\r
+ // and register with the applet so it can pass external API calls to us\r
+ jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,\r
+ DEFAULT_HEIGHT);\r
}\r
- else if (source == embeddedSelect)\r
+ }\r
+\r
+ /**\r
+ * create a new binding between structures in an existing jmol viewer instance\r
+ * and an alignpanel with sequences that have existing PDBFile entries. Note,\r
+ * this does not open a new Jmol window, or modify the display of the\r
+ * structures in the original jmol window. Note This method doesn't work\r
+ * without an additional javascript library to exchange messages between the\r
+ * distinct applets. See http://issues.jalview.org/browse/JAL-621\r
+ * \r
+ * @param viewer\r
+ * JmolViewer instance\r
+ * @param sequenceIds\r
+ * - sequence Ids to search for associations\r
+ */\r
+ public SequenceStructureBinding addStructureViewInstance(\r
+ Object jmolviewer, String[] sequenceIds)\r
+ {\r
+ org.jmol.api.JmolViewer viewer = null;\r
+ try\r
{\r
- popup = searchPopup = genPopupMenu(searchPopup, selectMenu);\r
+ viewer = (org.jmol.api.JmolViewer) jmolviewer;\r
+ } catch (ClassCastException ex)\r
+ {\r
+ System.err.println("Unsupported viewer object :"\r
+ + jmolviewer.getClass());\r
}\r
- else if (source == embeddedView)\r
+ if (viewer == null)\r
{\r
- popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
+ System.err.println("Can't use this object as a structure viewer:"\r
+ + jmolviewer.getClass());\r
+ return null;\r
}\r
- else if (source == embeddedFormat)\r
+ SequenceI[] seqs = null;\r
+ if (sequenceIds == null || sequenceIds.length == 0)\r
{\r
- popup = formatPopup = genPopupMenu(formatPopup, formatMenu);\r
+ seqs = viewport.getAlignment().getSequencesArray();\r
}\r
- else if (source == embeddedColour)\r
+ else\r
{\r
- popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
+ Vector sqi = new Vector();\r
+ AlignmentI al = viewport.getAlignment();\r
+ for (int sid = 0; sid < sequenceIds.length; sid++)\r
+ {\r
+ SequenceI sq = al.findName(sequenceIds[sid]);\r
+ if (sq != null)\r
+ {\r
+ sqi.addElement(sq);\r
+ }\r
+ }\r
+ if (sqi.size() > 0)\r
+ {\r
+ seqs = new SequenceI[sqi.size()];\r
+ for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)\r
+ {\r
+ seqs[sid] = (SequenceI) sqi.elementAt(sid);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ return null;\r
+ }\r
+ }\r
+ ExtJmol jmv = null;\r
+ // TODO: search for a jmv that involves viewer\r
+ if (jmv == null)\r
+ { // create a new viewer/jalview binding.\r
+ jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] {seqs});\r
}\r
- else if (source == embeddedCalculate)\r
+ return jmv;\r
+\r
+ }\r
+ /**\r
+ * bind a pdb file to a sequence in the current view\r
+ * \r
+ * @param sequenceId\r
+ * - sequenceId within the dataset.\r
+ * @param pdbEntryString\r
+ * - the short name for the PDB file\r
+ * @param pdbFile\r
+ * - pdb file - either a URL or a valid PDB file.\r
+ * @return true if binding was as success TODO: consider making an exception\r
+ * structure for indicating when PDB parsing or sequenceId location\r
+ * fails.\r
+ */\r
+ public boolean addPdbFile(String sequenceId, String pdbEntryString,\r
+ String pdbFile)\r
+ {\r
+ SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);\r
+ boolean needtoadd = false;\r
+ if (toaddpdb != null)\r
{\r
- popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
+ Vector pdbe = toaddpdb.getPDBId();\r
+ PDBEntry pdbentry = null;\r
+ if (pdbe != null && pdbe.size() > 0)\r
+ {\r
+ for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)\r
+ {\r
+ pdbentry = (PDBEntry) pdbe.elementAt(pe);\r
+ if (!pdbentry.getId().equals(pdbEntryString)\r
+ && !pdbentry.getFile().equals(pdbFile))\r
+ {\r
+ pdbentry = null;\r
+ }\r
+ else\r
+ {\r
+ continue;\r
+ }\r
+ }\r
+ }\r
+ if (pdbentry == null)\r
+ {\r
+ pdbentry = new PDBEntry();\r
+ pdbentry.setId(pdbEntryString);\r
+ pdbentry.setFile(pdbFile);\r
+ needtoadd = true; // add this new entry to sequence.\r
+ }\r
+ // resolve data source\r
+ // TODO: this code should be a refactored to an io package\r
+ String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");\r
+ if (protocol == null)\r
+ {\r
+ return false;\r
+ }\r
+ if (needtoadd)\r
+ {\r
+ // make a note of the access mode and add\r
+ if (pdbentry.getProperty() == null)\r
+ {\r
+ pdbentry.setProperty(new Hashtable());\r
+ }\r
+ pdbentry.getProperty().put("protocol", protocol);\r
+ toaddpdb.addPDBId(pdbentry);\r
+ }\r
}\r
- else if (source == embeddedHelp)\r
+ return true;\r
+ }\r
+\r
+ private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)\r
+ {\r
+ if (seqs != null)\r
{\r
- popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
+ Vector sequences = new Vector();\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if (seqs[i] != null)\r
+ {\r
+ sequences.addElement(new Object[]\r
+ { seqs[i], (chains != null) ? chains[i] : null });\r
+ }\r
+ }\r
+ seqs = new SequenceI[sequences.size()];\r
+ chains = new String[sequences.size()];\r
+ for (int i = 0, isize = sequences.size(); i < isize; i++)\r
+ {\r
+ Object[] oj = (Object[]) sequences.elementAt(i);\r
+\r
+ seqs[i] = (SequenceI) oj[0];\r
+ chains[i] = (String) oj[1];\r
+ }\r
}\r
+ return new Object[]\r
+ { seqs, chains };\r
\r
- embeddedMenu.add(popup);\r
- popup.show(embeddedMenu,\r
- source.getBounds().x,\r
- source.getBounds().y + source.getBounds().getSize().height);\r
}\r
\r
- PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
+ public void newStructureView(JalviewLite applet, PDBEntry pdb,\r
+ SequenceI[] seqs, String[] chains, String protocol)\r
{\r
- if (popup != null)\r
+ // Scrub any null sequences from the array\r
+ Object[] sqch = cleanSeqChainArrays(seqs, chains);\r
+ seqs = (SequenceI[]) sqch[0];\r
+ chains = (String[]) sqch[1];\r
+ if (seqs == null || seqs.length == 0)\r
+ {\r
+ System.err\r
+ .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");\r
+ }\r
+ if (protocol == null || protocol.trim().length() == 0\r
+ || protocol.equals("null"))\r
+ {\r
+ protocol = (String) pdb.getProperty().get("protocol");\r
+ if (protocol == null)\r
+ {\r
+ System.err.println("Couldn't work out protocol to open structure: "\r
+ + pdb.getId());\r
+ return;\r
+ }\r
+ }\r
+ if (applet.useXtrnalSviewer)\r
+ {\r
+ // register the association(s) and quit, don't create any windows.\r
+ if (StructureSelectionManager.getStructureSelectionManager(applet).setMapping(seqs, chains, pdb.getFile(), protocol)==null) {\r
+ System.err.println("Failed to map "+pdb.getFile()+" ("+protocol+") to any sequences");\r
+ }\r
+ return;\r
+ }\r
+ if (applet.isAlignPdbStructures() && applet.jmolAvailable)\r
+ {\r
+ // can only do alignments with Jmol\r
+ // find the last jmol window assigned to this alignment\r
+ jalview.appletgui.AppletJmol ajm = null, tajm;\r
+ Vector jmols = applet\r
+ .getAppletWindow(jalview.appletgui.AppletJmol.class);\r
+ for (int i = 0, iSize = jmols.size(); i < iSize; i++)\r
+ {\r
+ tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);\r
+ if (tajm.ap.alignFrame == this)\r
+ {\r
+ ajm = tajm;\r
+ break;\r
+ }\r
+ }\r
+ if (ajm != null)\r
+ {\r
+ System.err\r
+ .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");\r
+ // try and add the pdb structure\r
+ // ajm.addS\r
+ ajm = null;\r
+ }\r
+ }\r
+ // otherwise, create a new window\r
+ if (applet.jmolAvailable)\r
{\r
- return popup;\r
+ new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,\r
+ protocol);\r
+ applet.lastFrameX += 40;\r
+ applet.lastFrameY += 40;\r
}\r
- popup = new PopupMenu();\r
- int m, mSize = original.getItemCount();\r
- for (m = 0; m < mSize; m++)\r
+ else\r
{\r
- popup.add(original.getItem(m));\r
- mSize--;\r
- m--;\r
+ new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);\r
}\r
\r
- return popup;\r
}\r
\r
- public void mouseClicked(MouseEvent evt)\r
- {}\r
-\r
- public void mouseReleased(MouseEvent evt)\r
- {}\r
-\r
- public void mouseEntered(MouseEvent evt)\r
- {}\r
+ public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,\r
+ SequenceI[][] seqs, String[][] chains, String[] protocols)\r
+ {\r
+ // TODO Auto-generated method stub\r
+ System.err.println("Aligned Structure View: Not yet implemented.");\r
+ }\r
\r
- public void mouseExited(MouseEvent evt)\r
- {}\r
+ /**\r
+ * modify the current selection, providing the user has not made a selection already.\r
+ * @param sel - sequences from this alignment \r
+ * @param csel - columns to be selected on the alignment\r
+ */\r
+ public void select(SequenceGroup sel, ColumnSelection csel)\r
+ {\r
+ alignPanel.seqPanel.selection(sel, csel, null);\r
+ }\r
\r
+ public void scrollTo(int row, int column)\r
+ {\r
+ alignPanel.seqPanel.scrollTo(row, column); \r
+ }\r
+ public void scrollToRow(int row)\r
+ {\r
+ alignPanel.seqPanel.scrollToRow(row); \r
+ }\r
+ public void scrollToColumn(int column)\r
+ {\r
+ alignPanel.seqPanel.scrollToColumn(column); \r
+ }\r
+ /**\r
+ * @return the alignments unique ID.\r
+ */\r
+ public String getSequenceSetId() {\r
+ return viewport.getSequenceSetId();\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff