+++ /dev/null
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-*/\r
-package jalview.jbappletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-\r
-public class GAlignFrame extends Frame {\r
- protected MenuBar alignFrameMenuBar = new MenuBar();\r
- protected Menu fileMenu = new Menu();\r
- protected MenuItem closeMenuItem = new MenuItem();\r
- protected Menu editMenu = new Menu();\r
- protected Menu viewMenu = new Menu();\r
- protected Menu colourMenu = new Menu();\r
- protected Menu calculateMenu = new Menu();\r
- protected MenuItem selectAllSequenceMenuItem = new MenuItem();\r
- protected MenuItem deselectAllSequenceMenuItem = new MenuItem();\r
- protected MenuItem invertSequenceMenuItem = new MenuItem();\r
- protected MenuItem remove2LeftMenuItem = new MenuItem();\r
- protected MenuItem remove2RightMenuItem = new MenuItem();\r
- protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
- protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
- protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
- protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
- protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
- protected MenuItem sortIDMenuItem = new MenuItem();\r
- protected MenuItem sortGroupMenuItem = new MenuItem();\r
- protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
- protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
- protected MenuItem PCAMenuItem = new MenuItem();\r
- protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
- protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- public Label statusBar = new Label();\r
- protected Menu outputTextboxMenu = new Menu();\r
- protected MenuItem clustalColour = new MenuItem();\r
- protected MenuItem zappoColour = new MenuItem();\r
- protected MenuItem taylorColour = new MenuItem();\r
- protected MenuItem hydrophobicityColour = new MenuItem();\r
- protected MenuItem helixColour = new MenuItem();\r
- protected MenuItem strandColour = new MenuItem();\r
- protected MenuItem turnColour = new MenuItem();\r
- protected MenuItem buriedColour = new MenuItem();\r
- protected MenuItem userDefinedColour = new MenuItem();\r
- protected MenuItem PIDColour = new MenuItem();\r
- protected MenuItem BLOSUM62Colour = new MenuItem();\r
- MenuItem njTreeBlosumMenuItem = new MenuItem();\r
- MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
- protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
- protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
- MenuItem overviewMenuItem = new MenuItem();\r
- protected MenuItem undoMenuItem = new MenuItem();\r
- protected MenuItem redoMenuItem = new MenuItem();\r
- protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
- MenuItem noColourmenuItem = new MenuItem();\r
- protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
- protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
- MenuItem findMenuItem = new MenuItem();\r
- Menu searchMenu = new Menu();\r
- protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
- protected MenuItem nucleotideColour = new MenuItem();\r
- MenuItem deleteGroups = new MenuItem();\r
- MenuItem delete = new MenuItem();\r
- MenuItem copy = new MenuItem();\r
- MenuItem cut = new MenuItem();\r
- Menu Menu1 = new Menu();\r
- MenuItem pasteNew = new MenuItem();\r
- MenuItem pasteThis = new MenuItem();\r
- protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
- protected MenuItem font = new MenuItem();\r
- protected CheckboxMenuItem dbref = new CheckboxMenuItem();\r
- protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
- protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
- protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
- MenuItem modifyPID = new MenuItem();\r
- MenuItem modifyConservation = new MenuItem();\r
- protected Menu sortByTreeMenu = new Menu();\r
- Menu sort = new Menu();\r
- Menu calculate = new Menu();\r
- MenuItem inputText = new MenuItem();\r
- Menu helpMenu = new Menu();\r
- MenuItem documentation = new MenuItem();\r
- MenuItem about = new MenuItem();\r
- protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
-\r
- public GAlignFrame() {\r
- try {\r
- jbInit();\r
- setMenuBar(alignFrameMenuBar);\r
-\r
- MenuItem item;\r
-\r
- // dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++) {\r
- item = new MenuItem((String) jalview.io.AppletFormatAdapter.formats.elementAt(\r
- i));\r
- item.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- saveAs_actionPerformed(e);\r
- }\r
- });\r
-\r
- item = new MenuItem((String) jalview.io.AppletFormatAdapter.formats.elementAt(\r
- i));\r
- item.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputTextboxMenu.add(item);\r
- }\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- }\r
- }\r
-\r
- private void jbInit() throws Exception {\r
- fileMenu.setLabel("File");\r
- closeMenuItem.setLabel("Close");\r
- closeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- closeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- editMenu.setLabel("Edit");\r
- viewMenu.setLabel("View");\r
- colourMenu.setLabel("Colour");\r
- calculateMenu.setLabel("Calculate");\r
- selectAllSequenceMenuItem.setLabel("Select all");\r
- selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- selectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- deselectAllSequenceMenuItem.setLabel("Deselect All");\r
- deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- deselectAllSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- invertSequenceMenuItem.setLabel("Invert Selection");\r
- invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- invertSequenceMenuItem_actionPerformed(e);\r
- }\r
- });\r
- remove2LeftMenuItem.setLabel("Remove Left");\r
- remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- remove2LeftMenuItem_actionPerformed(e);\r
- }\r
- });\r
- remove2RightMenuItem.setLabel("Remove Right");\r
- remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- remove2RightMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
- removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- removeGappedColumnMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
- removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- removeAllGapsMenuItem_actionPerformed(e);\r
- }\r
- });\r
- viewBoxesMenuItem.setLabel("Boxes");\r
- viewBoxesMenuItem.setState(true);\r
- viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- viewBoxesMenuItem_actionPerformed(null);\r
- }\r
- });\r
- viewTextMenuItem.setLabel("Text");\r
- viewTextMenuItem.setState(true);\r
- viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- viewTextMenuItem_actionPerformed(null);\r
- }\r
- });\r
- sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
- sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- sortPairwiseMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortIDMenuItem.setLabel("by ID");\r
- sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- sortIDMenuItem_actionPerformed(e);\r
- }\r
- });\r
- sortGroupMenuItem.setLabel("by Group");\r
- sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- sortGroupMenuItem_actionPerformed(e);\r
- }\r
- });\r
- removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
- removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- removeRedundancyMenuItem_actionPerformed(e);\r
- }\r
- });\r
- pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
- pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- pairwiseAlignmentMenuItem_actionPerformed(e);\r
- }\r
- });\r
- PCAMenuItem.setLabel("Principal Component Analysis");\r
- PCAMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- PCAMenuItem_actionPerformed(e);\r
- }\r
- });\r
- averageDistanceTreeMenuItem.setLabel(\r
- "Average Distance Using % Identity");\r
- averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- averageDistanceTreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
- neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- neighbourTreeMenuItem_actionPerformed(e);\r
- }\r
- });\r
- alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setBackground(Color.white);\r
- statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
- statusBar.setText("Status bar");\r
- outputTextboxMenu.setLabel("Output to Textbox");\r
- clustalColour.setLabel("Clustalx");\r
-\r
- clustalColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- clustalColour_actionPerformed(e);\r
- }\r
- });\r
- zappoColour.setLabel("Zappo");\r
- zappoColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- zappoColour_actionPerformed(e);\r
- }\r
- });\r
- taylorColour.setLabel("Taylor");\r
- taylorColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- taylorColour_actionPerformed(e);\r
- }\r
- });\r
- hydrophobicityColour.setLabel("Hydrophobicity");\r
- hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- hydrophobicityColour_actionPerformed(e);\r
- }\r
- });\r
- helixColour.setLabel("Helix Propensity");\r
- helixColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- helixColour_actionPerformed(e);\r
- }\r
- });\r
- strandColour.setLabel("Strand Propensity");\r
- strandColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- strandColour_actionPerformed(e);\r
- }\r
- });\r
- turnColour.setLabel("Turn Propensity");\r
- turnColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- turnColour_actionPerformed(e);\r
- }\r
- });\r
- buriedColour.setLabel("Buried Index");\r
- buriedColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- buriedColour_actionPerformed(e);\r
- }\r
- });\r
- userDefinedColour.setLabel("User Defined...");\r
- userDefinedColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- userDefinedColour_actionPerformed(e);\r
- }\r
- });\r
- PIDColour.setLabel("Percentage Identity");\r
- PIDColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- PIDColour_actionPerformed(e);\r
- }\r
- });\r
- BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- BLOSUM62Colour_actionPerformed(e);\r
- }\r
- });\r
- avDistanceTreeBlosumMenuItem.setLabel(\r
- "Average Distance Using BLOSUM62");\r
- avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- avTreeBlosumMenuItem_actionPerformed(e);\r
- }\r
- });\r
- njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
- njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- njTreeBlosumMenuItem_actionPerformed(e);\r
- }\r
- });\r
- annotationPanelMenuItem.setActionCommand("");\r
- annotationPanelMenuItem.setState(true);\r
- annotationPanelMenuItem.setLabel("Show Annotations");\r
- annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- annotationPanelMenuItem_actionPerformed(null);\r
- }\r
- });\r
- colourTextMenuItem.setLabel("Colour Text");\r
- colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- colourTextMenuItem_actionPerformed(null);\r
- }\r
- });\r
- overviewMenuItem.setLabel("Overview Window");\r
- overviewMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- overviewMenuItem_actionPerformed(e);\r
- }\r
- });\r
- undoMenuItem.setEnabled(false);\r
- undoMenuItem.setLabel("Undo");\r
- undoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- undoMenuItem_actionPerformed(e);\r
- }\r
- });\r
- redoMenuItem.setEnabled(false);\r
- redoMenuItem.setLabel("Redo");\r
- redoMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- redoMenuItem_actionPerformed(e);\r
- }\r
- });\r
- conservationMenuItem.setLabel("by Conservation");\r
- conservationMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- conservationMenuItem_actionPerformed(null);\r
- }\r
- });\r
- noColourmenuItem.setLabel("None");\r
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- noColourmenuItem_actionPerformed(e);\r
- }\r
- });\r
- wrapMenuItem.setLabel("Wrap");\r
- wrapMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- wrapMenuItem_actionPerformed(null);\r
- }\r
- });\r
- renderGapsMenuItem.setLabel("Show Gaps");\r
- renderGapsMenuItem.setState(true);\r
- renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- renderGapsMenuItem_actionPerformed(null);\r
- }\r
- });\r
- findMenuItem.setLabel("Find...");\r
- findMenuItem.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- findMenuItem_actionPerformed(e);\r
- }\r
- });\r
- searchMenu.setLabel("Search");\r
-\r
- abovePIDThreshold.setLabel("Above Identity Threshold");\r
- abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- abovePIDThreshold_actionPerformed(null);\r
- }\r
- });\r
- nucleotideColour.setLabel("Nucleotide");\r
- nucleotideColour.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- nucleotideColour_actionPerformed(e);\r
- }\r
- });\r
- deleteGroups.setLabel("Undefine Groups");\r
- deleteGroups.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- deleteGroups_actionPerformed(e);\r
- }\r
- });\r
- copy.setLabel("Copy");\r
- copy.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- copy_actionPerformed(e);\r
- }\r
- });\r
- cut.setLabel("Cut");\r
- cut.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- cut_actionPerformed(e);\r
- }\r
- });\r
- delete.setLabel("Delete");\r
- delete.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- delete_actionPerformed(e);\r
- }\r
- });\r
- Menu1.setLabel("Paste");\r
- pasteNew.setLabel("To New Alignment");\r
- pasteNew.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- pasteNew_actionPerformed(e);\r
- }\r
- });\r
- pasteThis.setLabel("Add To This Alignment");\r
- pasteThis.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- pasteThis_actionPerformed(e);\r
- }\r
- });\r
- applyToAllGroups.setLabel("Apply Colour To All Groups");\r
- applyToAllGroups.setState(true);\r
- applyToAllGroups.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- applyToAllGroups_actionPerformed(null);\r
- }\r
- });\r
- font.setLabel("Font...");\r
- font.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- font_actionPerformed(e);\r
- }\r
- });\r
- dbref.setLabel("ShowSequence DB Refs");\r
- dbref.setActionCommand("");\r
- dbref.setState(true);\r
- dbref.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- dbref_actionPerformed(e);\r
- }\r
- });\r
- scaleAbove.setLabel("Scale Above");\r
- scaleAbove.setState(true);\r
- scaleAbove.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- scaleAbove_actionPerformed(null);\r
- }\r
- });\r
- scaleLeft.setEnabled(false);\r
- scaleLeft.setState(true);\r
- scaleLeft.setLabel("Scale Left");\r
- scaleLeft.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- scaleLeft_actionPerformed(null);\r
- }\r
- });\r
- scaleRight.setEnabled(false);\r
- scaleRight.setState(true);\r
- scaleRight.setLabel("Scale Right");\r
- scaleRight.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- scaleRight_actionPerformed(null);\r
- }\r
- });\r
- modifyPID.setLabel("Modify Identity Threshold...");\r
- modifyPID.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- modifyPID_actionPerformed(e);\r
- }\r
- });\r
- modifyConservation.setLabel("Modify Conservation Threshold...");\r
- modifyConservation.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- modifyConservation_actionPerformed(e);\r
- }\r
- });\r
- sortByTreeMenu.setLabel("By Tree Order");\r
- sort.setLabel("Sort");\r
- calculate.setLabel("Calculate Tree");\r
- inputText.setLabel("Input from textbox");\r
- inputText.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- inputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- helpMenu.setLabel("Help");\r
- documentation.setLabel("Documentation");\r
- documentation.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- documentation_actionPerformed(e);\r
- }\r
- });\r
-\r
- about.setLabel("About...");\r
- about.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- about_actionPerformed(e);\r
- }\r
- });\r
- seqLimits.setState(true);\r
- seqLimits.setLabel("Show Sequence Limits");\r
- seqLimits.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- seqLimits_itemStateChanged(e);\r
- }\r
- });\r
-\r
- alignFrameMenuBar.add(fileMenu);\r
- alignFrameMenuBar.add(editMenu);\r
- alignFrameMenuBar.add(searchMenu);\r
- alignFrameMenuBar.add(viewMenu);\r
- alignFrameMenuBar.add(colourMenu);\r
- alignFrameMenuBar.add(calculateMenu);\r
- alignFrameMenuBar.add(helpMenu);\r
- fileMenu.add(inputText);\r
- fileMenu.add(outputTextboxMenu);\r
- fileMenu.addSeparator();\r
- fileMenu.add(closeMenuItem);\r
- editMenu.add(undoMenuItem);\r
- editMenu.add(redoMenuItem);\r
- editMenu.add(cut);\r
- editMenu.add(copy);\r
- editMenu.add(Menu1);\r
- editMenu.add(delete);\r
- editMenu.addSeparator();\r
- editMenu.add(selectAllSequenceMenuItem);\r
- editMenu.add(deselectAllSequenceMenuItem);\r
- editMenu.add(invertSequenceMenuItem);\r
- editMenu.add(deleteGroups);\r
- editMenu.addSeparator();\r
- editMenu.add(remove2LeftMenuItem);\r
- editMenu.add(remove2RightMenuItem);\r
- editMenu.add(removeGappedColumnMenuItem);\r
- editMenu.add(removeAllGapsMenuItem);\r
- editMenu.add(removeRedundancyMenuItem);\r
- searchMenu.add(findMenuItem);\r
- viewMenu.add(font);\r
- viewMenu.addSeparator();\r
- viewMenu.add(dbref);\r
- viewMenu.add(seqLimits);\r
- viewMenu.addSeparator();\r
- viewMenu.add(wrapMenuItem);\r
- viewMenu.add(scaleAbove);\r
- viewMenu.add(scaleLeft);\r
- viewMenu.add(scaleRight);\r
- viewMenu.addSeparator();\r
- viewMenu.add(viewBoxesMenuItem);\r
- viewMenu.add(viewTextMenuItem);\r
- viewMenu.add(colourTextMenuItem);\r
- viewMenu.add(renderGapsMenuItem);\r
- viewMenu.add(annotationPanelMenuItem);\r
- viewMenu.addSeparator();\r
- viewMenu.add(overviewMenuItem);\r
- colourMenu.add(applyToAllGroups);\r
- colourMenu.addSeparator();\r
- colourMenu.add(noColourmenuItem);\r
- colourMenu.add(clustalColour);\r
- colourMenu.add(BLOSUM62Colour);\r
- colourMenu.add(PIDColour);\r
- colourMenu.add(zappoColour);\r
- colourMenu.add(taylorColour);\r
- colourMenu.add(hydrophobicityColour);\r
- colourMenu.add(helixColour);\r
- colourMenu.add(strandColour);\r
- colourMenu.add(turnColour);\r
- colourMenu.add(buriedColour);\r
- colourMenu.add(nucleotideColour);\r
- colourMenu.add(userDefinedColour);\r
- colourMenu.addSeparator();\r
- colourMenu.add(conservationMenuItem);\r
- colourMenu.add(modifyConservation);\r
- colourMenu.add(abovePIDThreshold);\r
- colourMenu.add(modifyPID);\r
- calculateMenu.add(sort);\r
- calculateMenu.add(calculate);\r
- calculateMenu.addSeparator();\r
- calculateMenu.add(pairwiseAlignmentMenuItem);\r
- calculateMenu.add(PCAMenuItem);\r
- this.add(statusBar, BorderLayout.SOUTH);\r
- Menu1.add(pasteNew);\r
- Menu1.add(pasteThis);\r
- sort.add(sortIDMenuItem);\r
- sort.add(sortByTreeMenu);\r
- sort.add(sortGroupMenuItem);\r
- sort.add(sortPairwiseMenuItem);\r
- calculate.add(averageDistanceTreeMenuItem);\r
- calculate.add(neighbourTreeMenuItem);\r
- calculate.add(avDistanceTreeBlosumMenuItem);\r
- calculate.add(njTreeBlosumMenuItem);\r
- helpMenu.add(documentation);\r
- helpMenu.add(about);\r
- }\r
-\r
- protected void saveAs_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void outputText_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void htmlMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void closeMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void redoMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void undoMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void invertSequenceMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void remove2LeftMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void remove2RightMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void removeAllGapsMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void viewBoxesMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void viewTextMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void annotationPanelMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void overviewMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void sortPairwiseMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void sortIDMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void sortGroupMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void removeRedundancyMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void PCAMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void neighbourTreeMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void clustalAlignMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void clustalColour_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void zappoColour_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void taylorColour_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void hydrophobicityColour_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void helixColour_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void strandColour_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void turnColour_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void buriedColour_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void userDefinedColour_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void PIDColour_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void printMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void findMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void abovePIDThreshold_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- public void sequenceFeatures_actionPerformed(ActionEvent actionEvent) {\r
- }\r
-\r
- protected void nucleotideColour_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void deleteGroups_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void copy_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void cut_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void delete_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void pasteNew_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void pasteThis_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void createPNG_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void font_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void epsFile_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void jpred_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void scaleAbove_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void scaleLeft_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void scaleRight_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void modifyPID_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void modifyConservation_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void preferences_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void inputText_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void documentation_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void about_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- public void dbref_actionPerformed(ItemEvent e)\r
- {\r
-\r
- }\r
-\r
- public void seqLimits_itemStateChanged(ItemEvent e)\r
- {\r
-\r
- }\r
-}\r
+++ /dev/null
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-*/\r
-package jalview.jbappletgui;\r
-\r
-import java.awt.*;\r
-\r
-\r
-public class GAlignmentPanel extends Panel {\r
- protected Panel sequenceHolderPanel = new Panel();\r
- protected Scrollbar vscroll = new Scrollbar();\r
- protected Scrollbar hscroll = new Scrollbar();\r
- protected Panel seqPanelHolder = new Panel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- BorderLayout borderLayout3 = new BorderLayout();\r
- protected Panel scalePanelHolder = new Panel();\r
- protected Panel idPanelHolder = new Panel();\r
- BorderLayout borderLayout5 = new BorderLayout();\r
- protected Panel idSpaceFillerPanel1 = new Panel();\r
- public Panel annotationSpaceFillerHolder = new Panel();\r
- BorderLayout borderLayout6 = new BorderLayout();\r
- BorderLayout borderLayout7 = new BorderLayout();\r
- Panel hscrollHolder = new Panel();\r
- BorderLayout borderLayout10 = new BorderLayout();\r
- protected Panel hscrollFillerPanel = new Panel();\r
- BorderLayout borderLayout11 = new BorderLayout();\r
- public Panel annotationScroller = new Panel();\r
- BorderLayout borderLayout4 = new BorderLayout();\r
- BorderLayout borderLayout2 = new BorderLayout();\r
-\r
- public GAlignmentPanel() {\r
- try {\r
- jbInit();\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- }\r
- }\r
-\r
- private void jbInit() throws Exception {\r
- // idPanelHolder.setPreferredSize(new Dimension(70, 10));\r
- this.setLayout(borderLayout7);\r
-\r
- // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));\r
- sequenceHolderPanel.setLayout(borderLayout3);\r
- seqPanelHolder.setLayout(borderLayout1);\r
- scalePanelHolder.setBackground(Color.white);\r
-\r
- // scalePanelHolder.setPreferredSize(new Dimension(10, 30));\r
- scalePanelHolder.setLayout(borderLayout6);\r
- idPanelHolder.setLayout(borderLayout5);\r
- idSpaceFillerPanel1.setBackground(Color.white);\r
-\r
- // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));\r
- idSpaceFillerPanel1.setLayout(borderLayout11);\r
- annotationSpaceFillerHolder.setBackground(Color.white);\r
-\r
- // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));\r
- annotationSpaceFillerHolder.setLayout(borderLayout4);\r
- hscroll.setOrientation(Scrollbar.HORIZONTAL);\r
- hscrollHolder.setLayout(borderLayout10);\r
- hscrollFillerPanel.setBackground(Color.white);\r
-\r
- // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));\r
- hscrollHolder.setBackground(Color.white);\r
-\r
- // annotationScroller.setPreferredSize(new Dimension(10, 80));\r
- // this.setPreferredSize(new Dimension(220, 166));\r
- seqPanelHolder.setBackground(Color.white);\r
- idPanelHolder.setBackground(Color.white);\r
- annotationScroller.setLayout(borderLayout2);\r
- sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);\r
- sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);\r
- seqPanelHolder.add(vscroll, BorderLayout.EAST);\r
- sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH);\r
-\r
- // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);\r
- this.add(idPanelHolder, BorderLayout.WEST);\r
- idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);\r
- idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);\r
- this.add(hscrollHolder, BorderLayout.SOUTH);\r
- hscrollHolder.add(hscroll, BorderLayout.CENTER);\r
- hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);\r
- this.add(sequenceHolderPanel, BorderLayout.CENTER);\r
- }\r
-}\r
+++ /dev/null
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-*/\r
-package jalview.jbappletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-\r
-public class GCutAndPasteTransfer extends Panel {\r
- protected TextArea textarea = new TextArea();\r
- Button ok = new Button();\r
- Button cancel = new Button();\r
- protected Panel buttonPanel = new Panel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
-\r
- public GCutAndPasteTransfer() {\r
- try {\r
- jbInit();\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- }\r
- }\r
-\r
- private void jbInit() throws Exception {\r
- textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10));\r
- textarea.setText("Paste your alignment file here");\r
- textarea.addMouseListener(new java.awt.event.MouseAdapter() {\r
- public void mousePressed(MouseEvent e) {\r
- textarea_mousePressed(e);\r
- }\r
- });\r
- this.setLayout(borderLayout1);\r
- ok.setLabel("OK");\r
- ok.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- ok_actionPerformed(e);\r
- }\r
- });\r
- cancel.setLabel("Cancel");\r
- cancel.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- cancel_actionPerformed(e);\r
- }\r
- });\r
- this.add(buttonPanel, BorderLayout.SOUTH);\r
- buttonPanel.add(ok, null);\r
- buttonPanel.add(cancel, null);\r
- this.add(textarea, java.awt.BorderLayout.CENTER);\r
- }\r
-\r
- void textarea_mousePressed(MouseEvent e) {\r
- if (textarea.getText().equals("Paste your alignment file here")) {\r
- textarea.setText("");\r
- }\r
- }\r
-\r
- protected void ok_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void cancel_actionPerformed(ActionEvent e) {\r
- }\r
-}\r
+++ /dev/null
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-*/\r
-package jalview.jbappletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-\r
-public class GFontChooser extends Panel {\r
- Label label1 = new Label();\r
- protected Choice fontSize = new Choice();\r
- protected Choice fontStyle = new Choice();\r
- Label label2 = new Label();\r
- Label label3 = new Label();\r
- protected Choice fontName = new Choice();\r
- Button ok = new Button();\r
- Button cancel = new Button();\r
- Panel panel1 = new Panel();\r
- Panel panel2 = new Panel();\r
- Panel panel3 = new Panel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- BorderLayout borderLayout2 = new BorderLayout();\r
- BorderLayout borderLayout3 = new BorderLayout();\r
- Panel panel4 = new Panel();\r
- Panel panel5 = new Panel();\r
- BorderLayout borderLayout4 = new BorderLayout();\r
-\r
- public GFontChooser() {\r
- try {\r
- jbInit();\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- }\r
- }\r
-\r
- private void jbInit() throws Exception {\r
- label1.setFont(new java.awt.Font("Verdana", 0, 11));\r
- label1.setAlignment(Label.RIGHT);\r
- label1.setText("Font: ");\r
- this.setLayout(borderLayout4);\r
- fontSize.setFont(new java.awt.Font("Verdana", 0, 11));\r
- fontSize.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- fontSize_actionPerformed();\r
- }\r
- });\r
- fontStyle.setFont(new java.awt.Font("Verdana", 0, 11));\r
- fontStyle.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- fontStyle_actionPerformed();\r
- }\r
- });\r
- label2.setAlignment(Label.RIGHT);\r
- label2.setFont(new java.awt.Font("Verdana", 0, 11));\r
- label2.setText("Size: ");\r
- label3.setAlignment(Label.RIGHT);\r
- label3.setFont(new java.awt.Font("Verdana", 0, 11));\r
- label3.setText("Style: ");\r
- fontName.setFont(new java.awt.Font("Verdana", 0, 11));\r
- fontName.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- fontName_actionPerformed();\r
- }\r
- });\r
- ok.setFont(new java.awt.Font("Verdana", 0, 11));\r
- ok.setLabel("OK");\r
- ok.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- ok_actionPerformed();\r
- }\r
- });\r
- cancel.setFont(new java.awt.Font("Verdana", 0, 11));\r
- cancel.setLabel("Cancel");\r
- cancel.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- cancel_actionPerformed();\r
- }\r
- });\r
- this.setBackground(Color.white);\r
- panel1.setLayout(borderLayout1);\r
- panel2.setLayout(borderLayout3);\r
- panel3.setLayout(borderLayout2);\r
- panel5.setBackground(Color.white);\r
- panel4.setBackground(Color.white);\r
- panel1.setBackground(Color.white);\r
- panel2.setBackground(Color.white);\r
- panel3.setBackground(Color.white);\r
- panel1.add(label1, BorderLayout.WEST);\r
- panel1.add(fontName, BorderLayout.CENTER);\r
- panel5.add(panel1, null);\r
- panel5.add(panel3, null);\r
- panel5.add(panel2, null);\r
- panel2.add(label3, BorderLayout.WEST);\r
- panel2.add(fontStyle, BorderLayout.CENTER);\r
- panel3.add(label2, BorderLayout.WEST);\r
- panel3.add(fontSize, BorderLayout.CENTER);\r
- this.add(panel4, BorderLayout.SOUTH);\r
- panel4.add(ok, null);\r
- panel4.add(cancel, null);\r
- this.add(panel5, BorderLayout.CENTER);\r
- }\r
-\r
- protected void ok_actionPerformed() {\r
- }\r
-\r
- protected void cancel_actionPerformed() {\r
- }\r
-\r
- protected void fontName_actionPerformed() {\r
- }\r
-\r
- protected void fontSize_actionPerformed() {\r
- }\r
-\r
- protected void fontStyle_actionPerformed() {\r
- }\r
-}\r
+++ /dev/null
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-*/\r
-package jalview.jbappletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-\r
-public class GPCAPanel extends Frame {\r
- Panel jPanel2 = new Panel();\r
- Label jLabel1 = new Label();\r
- Label jLabel2 = new Label();\r
- Label jLabel3 = new Label();\r
- protected Choice xCombobox = new Choice();\r
- protected Choice yCombobox = new Choice();\r
- protected Choice zCombobox = new Choice();\r
- FlowLayout flowLayout1 = new FlowLayout();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- MenuBar menuBar1 = new MenuBar();\r
- Menu menu1 = new Menu();\r
- Menu menu2 = new Menu();\r
- protected CheckboxMenuItem labels = new CheckboxMenuItem();\r
- MenuItem values = new MenuItem();\r
-\r
- public GPCAPanel() {\r
- try {\r
- jbInit();\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- }\r
-\r
- for (int i = 1; i < 8; i++) {\r
- xCombobox.addItem("dim " + i);\r
- yCombobox.addItem("dim " + i);\r
- zCombobox.addItem("dim " + i);\r
- }\r
- }\r
-\r
- private void jbInit() throws Exception {\r
- this.setLayout(borderLayout1);\r
- jPanel2.setLayout(flowLayout1);\r
- jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jLabel1.setText("x=");\r
- jLabel2.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jLabel2.setText("y=");\r
- jLabel3.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jLabel3.setText("z=");\r
- jPanel2.setBackground(Color.white);\r
- zCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
- zCombobox.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- zCombobox_actionPerformed(null);\r
- }\r
- });\r
- yCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
- yCombobox.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- yCombobox_actionPerformed(null);\r
- }\r
- });\r
- xCombobox.setFont(new java.awt.Font("Verdana", 0, 12));\r
- xCombobox.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- xCombobox_actionPerformed(null);\r
- }\r
- });\r
- this.setMenuBar(menuBar1);\r
- menu1.setLabel("File");\r
- menu2.setLabel("View");\r
- labels.setLabel("Labels");\r
- labels.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent itemEvent)\r
- {\r
- labels_itemStateChanged(itemEvent);\r
- }\r
- });\r
- values.setLabel("Output Values...");\r
- values.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent actionEvent)\r
- {\r
- values_actionPerformed(actionEvent);\r
- }\r
- });\r
- this.add(jPanel2, BorderLayout.SOUTH);\r
- jPanel2.add(jLabel1, null);\r
- jPanel2.add(xCombobox, null);\r
- jPanel2.add(jLabel2, null);\r
- jPanel2.add(yCombobox, null);\r
- jPanel2.add(jLabel3, null);\r
- jPanel2.add(zCombobox, null);\r
- menuBar1.add(menu1);\r
- menuBar1.add(menu2);\r
- menu2.add(labels);\r
- menu1.add(values);\r
- }\r
-\r
- protected void xCombobox_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void yCombobox_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void zCombobox_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- public void values_actionPerformed(ActionEvent actionEvent)\r
- {\r
-\r
- }\r
-\r
- public void labels_itemStateChanged(ItemEvent itemEvent)\r
- {\r
-\r
- }\r
-}\r
+++ /dev/null
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-*/\r
-package jalview.jbappletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-\r
-public class GPairwiseAlignPanel extends Panel {\r
- protected ScrollPane scrollPane = new ScrollPane();\r
- protected TextArea textarea = new TextArea();\r
- protected Button viewInEditorButton = new Button();\r
- Panel jPanel1 = new Panel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
-\r
- public GPairwiseAlignPanel() {\r
- try {\r
- jbInit();\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- }\r
- }\r
-\r
- private void jbInit() throws Exception {\r
- this.setLayout(borderLayout1);\r
- textarea.setFont(new java.awt.Font("Monospaced", 0, 12));\r
- textarea.setText("");\r
- viewInEditorButton.setFont(new java.awt.Font("Verdana", 0, 12));\r
- viewInEditorButton.setLabel("View in alignment editor");\r
- viewInEditorButton.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- viewInEditorButton_actionPerformed(e);\r
- }\r
- });\r
- this.add(scrollPane, BorderLayout.CENTER);\r
- scrollPane.add(textarea);\r
- this.add(jPanel1, BorderLayout.SOUTH);\r
- jPanel1.add(viewInEditorButton, null);\r
- }\r
-\r
- protected void viewInEditorButton_actionPerformed(ActionEvent e) {\r
- }\r
-}\r
+++ /dev/null
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-*/\r
-package jalview.jbappletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-\r
-public class GTreePanel extends Frame {\r
- BorderLayout borderLayout1 = new BorderLayout();\r
- protected ScrollPane scrollPane = new ScrollPane();\r
- MenuBar jMenuBar1 = new MenuBar();\r
- Menu jMenu2 = new Menu();\r
- protected MenuItem fontSize = new MenuItem();\r
- protected CheckboxMenuItem bootstrapMenu = new CheckboxMenuItem();\r
- protected CheckboxMenuItem distanceMenu = new CheckboxMenuItem();\r
- protected CheckboxMenuItem placeholdersMenu = new CheckboxMenuItem();\r
- protected CheckboxMenuItem fitToWindow = new CheckboxMenuItem();\r
- Menu fileMenu = new Menu();\r
- MenuItem newickOutput = new MenuItem();\r
-\r
- public GTreePanel() {\r
- try {\r
- jbInit();\r
- this.setMenuBar(jMenuBar1);\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- }\r
- }\r
-\r
- private void jbInit() throws Exception {\r
- setLayout(borderLayout1);\r
- this.setBackground(Color.white);\r
- this.setFont(new java.awt.Font("Verdana", 0, 12));\r
- jMenu2.setLabel("View");\r
- fontSize.setLabel("Font...");\r
- fontSize.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- fontSize_actionPerformed(e);\r
- }\r
- });\r
- bootstrapMenu.setLabel("Show Bootstrap Values");\r
- bootstrapMenu.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- bootstrapMenu_actionPerformed(null);\r
- }\r
- });\r
- distanceMenu.setLabel("Show Distances");\r
- distanceMenu.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- distanceMenu_actionPerformed(null);\r
- }\r
- });\r
- placeholdersMenu.setLabel("Mark Unassociated Leaves");\r
- placeholdersMenu.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- placeholdersMenu_actionPerformed(null);\r
- }\r
- });\r
- fitToWindow.setState(true);\r
- fitToWindow.setLabel("Fit To Window");\r
- fitToWindow.addItemListener(new java.awt.event.ItemListener() {\r
- public void itemStateChanged(ItemEvent e) {\r
- fitToWindow_actionPerformed(null);\r
- }\r
- });\r
- fileMenu.setLabel("File");\r
- newickOutput.setLabel("Newick Format");\r
- newickOutput.addActionListener(new ActionListener() {\r
- public void actionPerformed(ActionEvent actionEvent) {\r
- newickOutput_actionPerformed(actionEvent);\r
- }\r
- });\r
- add(scrollPane, BorderLayout.CENTER);\r
- jMenuBar1.add(fileMenu);\r
- jMenuBar1.add(jMenu2);\r
- jMenu2.add(fitToWindow);\r
- jMenu2.add(fontSize);\r
- jMenu2.add(distanceMenu);\r
- jMenu2.add(bootstrapMenu);\r
- jMenu2.add(placeholdersMenu);\r
- fileMenu.add(newickOutput);\r
- }\r
-\r
- protected void printMenu_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void fontSize_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void distanceMenu_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void bootstrapMenu_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void placeholdersMenu_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void fitToWindow_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- public void newickOutput_actionPerformed(ActionEvent actionEvent) {\r
- }\r
-}\r
+++ /dev/null
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-*/\r
-package jalview.jbappletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-\r
-public class GUserDefinedColours extends Panel {\r
- protected Panel buttonPanel = new Panel();\r
- protected GridLayout gridLayout = new GridLayout();\r
- Panel jPanel2 = new Panel();\r
- protected Button okButton = new Button();\r
- protected Button applyButton = new Button();\r
- protected Button cancelButton = new Button();\r
- protected Scrollbar rScroller = new Scrollbar();\r
- Label label1 = new Label();\r
- protected TextField rText = new TextField();\r
- Label label4 = new Label();\r
- protected Scrollbar gScroller = new Scrollbar();\r
- protected TextField gText = new TextField();\r
- Label label5 = new Label();\r
- protected Scrollbar bScroller = new Scrollbar();\r
- protected TextField bText = new TextField();\r
- protected Panel target = new Panel();\r
-\r
- public GUserDefinedColours() {\r
- try {\r
- jbInit();\r
- } catch (Exception e) {\r
- e.printStackTrace();\r
- }\r
- }\r
-\r
- private void jbInit() throws Exception {\r
- this.setLayout(null);\r
- buttonPanel.setLayout(gridLayout);\r
- gridLayout.setColumns(6);\r
- gridLayout.setRows(4);\r
- okButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
- okButton.setLabel("OK");\r
- okButton.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- okButton_actionPerformed(e);\r
- }\r
- });\r
- applyButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
- applyButton.setLabel("Apply");\r
- applyButton.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- applyButton_actionPerformed(e);\r
- }\r
- });\r
- cancelButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
- cancelButton.setLabel("Cancel");\r
- cancelButton.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- cancelButton_actionPerformed(e);\r
- }\r
- });\r
- this.setBackground(new Color(212, 208, 223));\r
- jPanel2.setBounds(new Rectangle(0, 265, 400, 35));\r
- buttonPanel.setBounds(new Rectangle(0, 123, 400, 142));\r
- rScroller.setMaximum(256);\r
- rScroller.setMinimum(0);\r
- rScroller.setOrientation(0);\r
- rScroller.setUnitIncrement(1);\r
- rScroller.setVisibleAmount(1);\r
- rScroller.setBounds(new Rectangle(36, 27, 119, 19));\r
- rScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {\r
- public void adjustmentValueChanged(AdjustmentEvent e) {\r
- rScroller_adjustmentValueChanged(e);\r
- }\r
- });\r
- label1.setAlignment(Label.RIGHT);\r
- label1.setText("R");\r
- label1.setBounds(new Rectangle(19, 30, 16, 15));\r
- rText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));\r
- rText.setText("0 ");\r
- rText.setBounds(new Rectangle(156, 27, 53, 19));\r
- rText.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- rText_actionPerformed(e);\r
- }\r
- });\r
- label4.setAlignment(Label.RIGHT);\r
- label4.setText("G");\r
- label4.setBounds(new Rectangle(15, 56, 20, 15));\r
- gScroller.setMaximum(256);\r
- gScroller.setMinimum(0);\r
- gScroller.setOrientation(0);\r
- gScroller.setUnitIncrement(1);\r
- gScroller.setVisibleAmount(1);\r
- gScroller.setBounds(new Rectangle(35, 52, 120, 20));\r
- gScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {\r
- public void adjustmentValueChanged(AdjustmentEvent e) {\r
- gScroller_adjustmentValueChanged(e);\r
- }\r
- });\r
- gText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));\r
- gText.setText("0 ");\r
- gText.setBounds(new Rectangle(156, 52, 53, 20));\r
- gText.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- gText_actionPerformed(e);\r
- }\r
- });\r
- label5.setAlignment(Label.RIGHT);\r
- label5.setText("B");\r
- label5.setBounds(new Rectangle(14, 82, 20, 15));\r
- bScroller.setMaximum(256);\r
- bScroller.setMinimum(0);\r
- bScroller.setOrientation(0);\r
- bScroller.setUnitIncrement(1);\r
- bScroller.setVisibleAmount(1);\r
- bScroller.setBounds(new Rectangle(35, 78, 120, 20));\r
- bScroller.addAdjustmentListener(new java.awt.event.AdjustmentListener() {\r
- public void adjustmentValueChanged(AdjustmentEvent e) {\r
- bScroller_adjustmentValueChanged(e);\r
- }\r
- });\r
- bText.setFont(new java.awt.Font("Dialog", Font.PLAIN, 10));\r
- bText.setText("0 ");\r
- bText.setBounds(new Rectangle(157, 78, 52, 20));\r
- bText.addActionListener(new java.awt.event.ActionListener() {\r
- public void actionPerformed(ActionEvent e) {\r
- bText_actionPerformed(e);\r
- }\r
- });\r
- target.setBackground(Color.black);\r
- target.setBounds(new Rectangle(229, 26, 134, 79));\r
- this.add(jPanel2, null);\r
- jPanel2.add(okButton, null);\r
- jPanel2.add(applyButton, null);\r
- jPanel2.add(cancelButton, null);\r
- this.add(buttonPanel, null);\r
- this.add(target, null);\r
- this.add(gScroller);\r
- this.add(rScroller);\r
- this.add(bScroller);\r
- this.add(label5);\r
- this.add(label4);\r
- this.add(label1);\r
- this.add(gText);\r
- this.add(rText);\r
- this.add(bText);\r
- }\r
-\r
- protected void okButton_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void applyButton_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void cancelButton_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void rScroller_adjustmentValueChanged(AdjustmentEvent e) {\r
- }\r
-\r
- protected void gScroller_adjustmentValueChanged(AdjustmentEvent e) {\r
- }\r
-\r
- protected void bScroller_adjustmentValueChanged(AdjustmentEvent e) {\r
- }\r
-\r
- protected void rText_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void gText_actionPerformed(ActionEvent e) {\r
- }\r
-\r
- protected void bText_actionPerformed(ActionEvent e) {\r
- }\r
-}\r
git://source.jalview.org / jalview.git / commitdiff