-package jalview.appletgui;
-
-import jalview.analysis.AlignmentUtils;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.ViewStyleI;
-import jalview.bin.JalviewLite;
-import jalview.datamodel.AlignmentI;
-import jalview.structure.StructureSelectionManager;
-import jalview.viewmodel.AlignmentViewport;
-
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.GridLayout;
-
-import javax.swing.JPanel;
-
-public class SplitFrame extends EmbmenuFrame
-{
- private static final long serialVersionUID = 1L;
-
- private AlignFrame topFrame;
-
- private AlignFrame bottomFrame;
-
- private JPanel outermost;
-
-
- /**
- * Constructor
- */
- public SplitFrame(AlignFrame af1, AlignFrame af2)
- {
- topFrame = af1;
- bottomFrame = af2;
- init();
- }
-
- /**
- * Creates a Panel containing two Panels, and adds the first and second
- * AlignFrame's components to each. At this stage we have not yet committed to
- * whether the enclosing panel will be added to this frame, for display as a
- * separate frame, or added to the applet (embedded mode).
- */
- public void init()
- {
- constructSplit();
-
- /*
- * Try to make and add dna/protein sequence mappings
- */
- final AlignViewport topViewport = topFrame.viewport;
- final AlignViewport bottomViewport = bottomFrame.viewport;
- final AlignmentI topAlignment = topViewport.getAlignment();
- final AlignmentI bottomAlignment = bottomViewport.getAlignment();
- AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport
- : (bottomAlignment.isNucleotide() ? bottomViewport : null);
- AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport
- : (!bottomAlignment.isNucleotide() ? bottomViewport : null);
-
- boolean mapped = AlignmentUtils.mapProteinToCdna(
- protein.getAlignment(), cdna.getAlignment());
- if (mapped)
- {
- final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(topViewport.applet);
- ssm.addMappings(protein.getAlignment().getCodonFrames());
- topViewport.setCodingComplement(bottomViewport);
- ssm.addCommandListener(cdna);
- ssm.addCommandListener(protein);
- }
-
- /*
- * Now mappings exist, can compute cDNA consensus on protein alignment
- */
- protein.initComplementConsensus();
- AlignmentViewPanel ap = topAlignment.isNucleotide() ? bottomFrame.alignPanel
- : topFrame.alignPanel;
- protein.updateConsensus(ap);
-
- adjustLayout();
- }
-
- /**
- *
- */
- protected void constructSplit()
- {
- setMenuBar(null);
- outermost = new JPanel(new GridLayout(2, 1));
-
- JPanel topPanel = new JPanel();
- JPanel bottomPanel = new JPanel();
- outermost.add(topPanel);
- outermost.add(bottomPanel);
-
- addAlignFrameComponents(topFrame, topPanel);
- addAlignFrameComponents(bottomFrame, bottomPanel);
- }
-
- /**
- * Make any adjustments to the layout
- */
- protected void adjustLayout()
- {
- AlignmentViewport cdna = topFrame.getAlignViewport().getAlignment()
- .isNucleotide() ? topFrame.viewport : bottomFrame.viewport;
- AlignmentViewport protein = cdna == topFrame.viewport ? bottomFrame.viewport
- : topFrame.viewport;
-
- /*
- * Ensure sequence ids are the same width for good alignment.
- */
- // TODO should do this via av.getViewStyle/setViewStyle
- // however at present av.viewStyle is not set in IdPanel.fontChanged
- int w1 = topFrame.alignPanel.idPanel.idCanvas.getWidth();
- int w2 = bottomFrame.alignPanel.idPanel.idCanvas.getWidth();
- int w3 = Math.max(w1, w2);
- if (w1 != w3)
- {
- Dimension d = topFrame.alignPanel.idPanel.idCanvas.getSize();
- topFrame.alignPanel.idPanel.idCanvas.setSize(new Dimension(w3,
- d.height));
- }
- if (w2 != w3)
- {
- Dimension d = bottomFrame.alignPanel.idPanel.idCanvas.getSize();
- bottomFrame.alignPanel.idPanel.idCanvas.setSize(new Dimension(w3,
- d.height));
- }
-
- /*
- * Scale protein to either 1 or 3 times character width of dna
- */
- if (protein != null && cdna != null)
- {
- ViewStyleI vs = protein.getViewStyle();
- int scale = vs.isScaleProteinAsCdna() ? 3 : 1;
- vs.setCharWidth(scale * cdna.getViewStyle().getCharWidth());
- protein.setViewStyle(vs);
- }
- }
-
- /**
- * Add the menu bar, alignment panel and status bar from the AlignFrame to the
- * panel. The menu bar is a panel 'reconstructed' from the AlignFrame's frame
- * menu bar. This allows each half of the SplitFrame to have its own menu bar.
- *
- * @param af
- * @param panel
- */
- private void addAlignFrameComponents(AlignFrame af, JPanel panel) {
- panel.setLayout(new BorderLayout());
- JPanel menuPanel = af.makeEmbeddedPopupMenu(af.getJMenuBar(), true, false);
- panel.add(menuPanel, BorderLayout.NORTH);
- panel.add(af.statusBar, BorderLayout.SOUTH);
- panel.add(af.alignPanel, BorderLayout.CENTER);
-
- af.setSplitFrame(this);
- }
-
- /**
- * Display the content panel either as a new frame or embedded in the applet.
- *
- * @param embedded
- * @param applet
- */
- public void addToDisplay(boolean embedded, JalviewLite applet)
- {
- createSplitFrameWindow(embedded, applet);
- validate();
- topFrame.alignPanel.adjustAnnotationHeight();
- topFrame.alignPanel.paintAlignment(true);
- bottomFrame.alignPanel.adjustAnnotationHeight();
- bottomFrame.alignPanel.paintAlignment(true);
- }
-
- /**
- * Either show the content panel in this frame as a new frame, or (if
- * embed=true) add it to the applet container instead.
- *
- * @param embed
- * @param applet
- */
- protected void createSplitFrameWindow(boolean embed, JalviewLite applet)
- {
- if (embed)
- {
- applet.add(outermost);
- applet.validate();
- }
- else
- {
- this.add(outermost);
- int width = Math.max(topFrame.frameWidth, bottomFrame.frameWidth);
- int height = topFrame.frameHeight + bottomFrame.frameHeight;
- JalviewLite.addFrame(this, this.getTitle(), width, height);
- }
- }
-
- /**
- * Returns the contained AlignFrame complementary to the one given (or null if
- * no match to top or bottom component).
- *
- * @param af
- * @return
- */
- public AlignFrame getComplement(AlignFrame af)
- {
- if (topFrame == af)
- {
- return bottomFrame;
- }
- else if (bottomFrame == af)
- {
- return topFrame;
- }
- return null;
- }
-}
+package jalview.appletgui;\r
+\r
+import jalview.analysis.AlignmentUtils;\r
+import jalview.api.AlignmentViewPanel;\r
+import jalview.api.ViewStyleI;\r
+import jalview.bin.JalviewLite;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.structure.StructureSelectionManager;\r
+import jalview.viewmodel.AlignmentViewport;\r
+\r
+import java.awt.BorderLayout;\r
+import java.awt.Dimension;\r
+import java.awt.GridLayout;\r
+\r
+import javax.swing.JPanel;\r
+\r
+public class SplitFrame extends EmbmenuFrame\r
+{\r
+ private static final long serialVersionUID = 1L;\r
+\r
+ private AlignFrame topFrame;\r
+\r
+ private AlignFrame bottomFrame;\r
+\r
+ private JPanel outermost;\r
+ \r
+\r
+ /**\r
+ * Constructor\r
+ */\r
+ public SplitFrame(AlignFrame af1, AlignFrame af2)\r
+ {\r
+ topFrame = af1;\r
+ bottomFrame = af2;\r
+ init();\r
+ }\r
+\r
+ /**\r
+ * Creates a Panel containing two Panels, and adds the first and second\r
+ * AlignFrame's components to each. At this stage we have not yet committed to\r
+ * whether the enclosing panel will be added to this frame, for display as a\r
+ * separate frame, or added to the applet (embedded mode).\r
+ */\r
+ public void init()\r
+ {\r
+ constructSplit();\r
+\r
+ /*\r
+ * Try to make and add dna/protein sequence mappings\r
+ */\r
+ final AlignViewport topViewport = topFrame.viewport;\r
+ final AlignViewport bottomViewport = bottomFrame.viewport;\r
+ final AlignmentI topAlignment = topViewport.getAlignment();\r
+ final AlignmentI bottomAlignment = bottomViewport.getAlignment();\r
+ AlignmentViewport cdna = topAlignment.isNucleotide() ? topViewport\r
+ : (bottomAlignment.isNucleotide() ? bottomViewport : null);\r
+ AlignmentViewport protein = !topAlignment.isNucleotide() ? topViewport\r
+ : (!bottomAlignment.isNucleotide() ? bottomViewport : null);\r
+\r
+ boolean mapped = AlignmentUtils.mapProteinToCdna(\r
+ protein.getAlignment(), cdna.getAlignment());\r
+ if (mapped)\r
+ {\r
+ final StructureSelectionManager ssm = StructureSelectionManager\r
+ .getStructureSelectionManager(topViewport.applet);\r
+ ssm.addMappings(protein.getAlignment().getCodonFrames());\r
+ topViewport.setCodingComplement(bottomViewport);\r
+ ssm.addCommandListener(cdna);\r
+ ssm.addCommandListener(protein);\r
+ }\r
+\r
+ /*\r
+ * Now mappings exist, can compute cDNA consensus on protein alignment\r
+ */\r
+ protein.initComplementConsensus();\r
+ AlignmentViewPanel ap = topAlignment.isNucleotide() ? bottomFrame.alignPanel\r
+ : topFrame.alignPanel;\r
+ protein.updateConsensus(ap);\r
+\r
+ adjustLayout();\r
+ }\r
+\r
+ /**\r
+ * \r
+ */\r
+ protected void constructSplit()\r
+ {\r
+ setMenuBar(null);\r
+ outermost = new JPanel(new GridLayout(2, 1));\r
+\r
+ JPanel topPanel = new JPanel();\r
+ JPanel bottomPanel = new JPanel();\r
+ outermost.add(topPanel);\r
+ outermost.add(bottomPanel);\r
+\r
+ addAlignFrameComponents(topFrame, topPanel);\r
+ addAlignFrameComponents(bottomFrame, bottomPanel);\r
+ }\r
+\r
+ /**\r
+ * Make any adjustments to the layout\r
+ */\r
+ protected void adjustLayout()\r
+ {\r
+ AlignmentViewport cdna = topFrame.getAlignViewport().getAlignment()\r
+ .isNucleotide() ? topFrame.viewport : bottomFrame.viewport;\r
+ AlignmentViewport protein = cdna == topFrame.viewport ? bottomFrame.viewport\r
+ : topFrame.viewport;\r
+\r
+ /*\r
+ * Ensure sequence ids are the same width for good alignment.\r
+ */\r
+ // TODO should do this via av.getViewStyle/setViewStyle\r
+ // however at present av.viewStyle is not set in IdPanel.fontChanged\r
+ int w1 = topFrame.alignPanel.idPanel.idCanvas.getWidth();\r
+ int w2 = bottomFrame.alignPanel.idPanel.idCanvas.getWidth();\r
+ int w3 = Math.max(w1, w2);\r
+ if (w1 != w3)\r
+ {\r
+ Dimension d = topFrame.alignPanel.idPanel.idCanvas.getSize();\r
+ topFrame.alignPanel.idPanel.idCanvas.setSize(new Dimension(w3,\r
+ d.height));\r
+ }\r
+ if (w2 != w3)\r
+ {\r
+ Dimension d = bottomFrame.alignPanel.idPanel.idCanvas.getSize();\r
+ bottomFrame.alignPanel.idPanel.idCanvas.setSize(new Dimension(w3,\r
+ d.height));\r
+ }\r
+\r
+ /*\r
+ * Scale protein to either 1 or 3 times character width of dna\r
+ */\r
+ if (protein != null && cdna != null)\r
+ {\r
+ ViewStyleI vs = protein.getViewStyle();\r
+ int scale = vs.isScaleProteinAsCdna() ? 3 : 1;\r
+ vs.setCharWidth(scale * cdna.getViewStyle().getCharWidth());\r
+ protein.setViewStyle(vs);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Add the menu bar, alignment panel and status bar from the AlignFrame to the\r
+ * panel. The menu bar is a panel 'reconstructed' from the AlignFrame's frame\r
+ * menu bar. This allows each half of the SplitFrame to have its own menu bar.\r
+ * \r
+ * @param af\r
+ * @param panel\r
+ */\r
+ private void addAlignFrameComponents(AlignFrame af, JPanel panel) {\r
+ panel.setLayout(new BorderLayout());\r
+ JPanel menuPanel = af.makeEmbeddedPopupMenu(af.getJMenuBar(), true, false);\r
+ panel.add(menuPanel, BorderLayout.NORTH);\r
+ panel.add(af.statusBar, BorderLayout.SOUTH);\r
+ panel.add(af.alignPanel, BorderLayout.CENTER);\r
+\r
+ af.setSplitFrame(this);\r
+ }\r
+\r
+ /**\r
+ * Display the content panel either as a new frame or embedded in the applet.\r
+ * \r
+ * @param embedded\r
+ * @param applet\r
+ */\r
+ public void addToDisplay(boolean embedded, JalviewLite applet)\r
+ {\r
+ createSplitFrameWindow(embedded, applet);\r
+ validate();\r
+ topFrame.alignPanel.adjustAnnotationHeight();\r
+ topFrame.alignPanel.paintAlignment(true);\r
+ bottomFrame.alignPanel.adjustAnnotationHeight();\r
+ bottomFrame.alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ /**\r
+ * Either show the content panel in this frame as a new frame, or (if\r
+ * embed=true) add it to the applet container instead.\r
+ * \r
+ * @param embed\r
+ * @param applet\r
+ */\r
+ protected void createSplitFrameWindow(boolean embed, JalviewLite applet)\r
+ {\r
+ if (embed)\r
+ {\r
+ applet.add(outermost);\r
+ applet.validate();\r
+ }\r
+ else\r
+ {\r
+ this.add(outermost);\r
+ int width = Math.max(topFrame.frameWidth, bottomFrame.frameWidth);\r
+ int height = topFrame.frameHeight + bottomFrame.frameHeight;\r
+ JalviewLite.addFrame(this, this.getTitle(), width, height);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Returns the contained AlignFrame complementary to the one given (or null if\r
+ * no match to top or bottom component).\r
+ * \r
+ * @param af\r
+ * @return\r
+ */\r
+ public AlignFrame getComplement(AlignFrame af)\r
+ {\r
+ if (topFrame == af)\r
+ {\r
+ return bottomFrame;\r
+ }\r
+ else if (bottomFrame == af)\r
+ {\r
+ return topFrame;\r
+ }\r
+ return null;\r
+ }\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff