-/*\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
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class AlignmentPanel\r
- extends Panel implements AdjustmentListener\r
-{\r
-\r
- public AlignViewport av;\r
- OverviewPanel overviewPanel;\r
- SeqPanel seqPanel;\r
- IdPanel idPanel;\r
- IdwidthAdjuster idwidthAdjuster;\r
- public AlignFrame alignFrame;\r
- ScalePanel scalePanel;\r
- AnnotationPanel annotationPanel;\r
- AnnotationLabels alabels;\r
-\r
- // this value is set false when selection area being dragged\r
- boolean fastPaint = true;\r
-\r
- public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception e)\r
- {\r
- e.printStackTrace();\r
- }\r
-\r
- alignFrame = af;\r
- this.av = av;\r
- seqPanel = new SeqPanel(av, this);\r
- idPanel = new IdPanel(av, this);\r
- scalePanel = new ScalePanel(av, this);\r
- idwidthAdjuster = new IdwidthAdjuster(this);\r
- annotationPanel = new AnnotationPanel(this);\r
-\r
- sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH);\r
-\r
- alabels = new AnnotationLabels(this);\r
-\r
- setAnnotationVisible(av.showAnnotation);\r
-\r
- idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
- idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);\r
- annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
- scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
- seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
-\r
- fontChanged();\r
- setScrollValues(0, 0);\r
-\r
- hscroll.addAdjustmentListener(this);\r
- vscroll.addAdjustmentListener(this);\r
-\r
- addComponentListener(new ComponentAdapter()\r
- {\r
- public void componentResized(ComponentEvent evt)\r
- {\r
- setScrollValues(av.getStartRes(), av.getStartSeq());\r
- repaint();\r
- }\r
- });\r
-\r
- Dimension d = calculateIdWidth();\r
- idPanel.idCanvas.setSize(d);\r
-\r
- hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);\r
-\r
- idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);\r
- annotationSpaceFillerHolder.setSize(d.width,\r
- annotationPanel.getSize().height);\r
- alabels.setSize(d.width, annotationPanel.getSize().height);\r
-\r
- final AlignmentPanel ap = this;\r
- av.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
- {\r
- public void propertyChange(java.beans.PropertyChangeEvent evt)\r
- {\r
- if (evt.getPropertyName().equals("alignment"))\r
- {\r
- PaintRefresher.Refresh(ap,\r
- av.getSequenceSetId(),\r
- true,\r
- true);\r
- alignmentChanged();\r
- }\r
- }\r
- });\r
-\r
- }\r
-\r
- public SequenceRenderer getSequenceRenderer()\r
- {\r
- return seqPanel.seqCanvas.sr;\r
- }\r
-\r
- public FeatureRenderer getFeatureRenderer()\r
- {\r
- return seqPanel.seqCanvas.fr;\r
- }\r
-\r
- public void alignmentChanged()\r
- {\r
- av.alignmentChanged(this);\r
-\r
- if (overviewPanel != null)\r
- {\r
- overviewPanel.updateOverviewImage();\r
- }\r
-\r
- alignFrame.updateEditMenuBar();\r
-\r
- repaint();\r
- }\r
-\r
- public void fontChanged()\r
- {\r
- // set idCanvas bufferedImage to null\r
- // to prevent drawing old image\r
- idPanel.idCanvas.image = null;\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
-\r
- scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));\r
- idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent()));\r
-\r
- annotationPanel.image = null;\r
- int ap = annotationPanel.adjustPanelHeight();\r
- annotationPanel.repaint();\r
- Dimension d = calculateIdWidth();\r
- d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);\r
- alabels.setSize(d.width + 4, ap);\r
- idPanel.idCanvas.setSize(d);\r
- hscrollFillerPanel.setSize(d);\r
-\r
- validate();\r
- repaint();\r
-\r
- if (overviewPanel != null)\r
- {\r
- overviewPanel.updateOverviewImage();\r
- }\r
- }\r
-\r
- public void setIdWidth(int w, int h)\r
- {\r
- idPanel.idCanvas.setSize(w, h);\r
- idPanelHolder.setSize(w, idPanelHolder.getSize().height);\r
- alabels.setSize(w, alabels.getSize().height);\r
- validate();\r
- }\r
-\r
- Dimension calculateIdWidth()\r
- {\r
- if (av.nullFrame == null)\r
- {\r
- av.nullFrame = new Frame();\r
- av.nullFrame.addNotify();\r
- }\r
-\r
- Graphics g = av.nullFrame.getGraphics();\r
-\r
- FontMetrics fm = g.getFontMetrics(av.font);\r
- AlignmentI al = av.getAlignment();\r
-\r
- int i = 0;\r
- int idWidth = 0;\r
- String id;\r
- while (i < al.getHeight() && al.getSequenceAt(i) != null)\r
- {\r
- SequenceI s = al.getSequenceAt(i);\r
- id = s.getDisplayId(av.getShowJVSuffix());\r
-\r
- if (fm.stringWidth(id) > idWidth)\r
- {\r
- idWidth = fm.stringWidth(id);\r
- }\r
- i++;\r
- }\r
-\r
- // Also check annotation label widths\r
- i = 0;\r
- if (al.getAlignmentAnnotation() != null)\r
- {\r
- fm = g.getFontMetrics(av.nullFrame.getFont());\r
- while (i < al.getAlignmentAnnotation().length)\r
- {\r
- String label = al.getAlignmentAnnotation()[i].label;\r
- if (fm.stringWidth(label) > idWidth)\r
- {\r
- idWidth = fm.stringWidth(label);\r
- }\r
- i++;\r
- }\r
- }\r
-\r
- return new Dimension(idWidth, idPanel.idCanvas.getSize().height);\r
- }\r
-\r
- public void highlightSearchResults(SearchResults results)\r
- {\r
- seqPanel.seqCanvas.highlightSearchResults(results);\r
-\r
- // do we need to scroll the panel?\r
- if (results != null)\r
- {\r
- SequenceI seq = results.getResultSequence(0);\r
- int seqIndex = av.alignment.findIndex(seq);\r
- int start = seq.findIndex(results.getResultStart(0)) - 1;\r
- int end = seq.findIndex(results.getResultEnd(0)) - 1;\r
-\r
- if (!av.wrapAlignment)\r
- {\r
- if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||\r
- ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))\r
- {\r
- if (start > av.alignment.getWidth() - hextent)\r
- {\r
- start = av.alignment.getWidth() - hextent;\r
- if (start < 0)\r
- {\r
- start = 0;\r
- }\r
- }\r
- if (seqIndex > av.alignment.getHeight() - vextent)\r
- {\r
- seqIndex = av.alignment.getHeight() - vextent;\r
- if (seqIndex < 0)\r
- {\r
- seqIndex = 0;\r
- }\r
- }\r
- setScrollValues(start, seqIndex);\r
- }\r
- }\r
- else\r
- {\r
- scrollToWrappedVisible(start);\r
- }\r
- }\r
-\r
- repaint();\r
- }\r
-\r
- void scrollToWrappedVisible(int res)\r
- {\r
- int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.\r
- getSize().width);\r
- if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))\r
- {\r
- vscroll.setValue(res / cwidth);\r
- av.startRes = vscroll.getValue() * cwidth;\r
- }\r
- }\r
-\r
- public OverviewPanel getOverviewPanel()\r
- {\r
- return overviewPanel;\r
- }\r
-\r
- public void setOverviewPanel(OverviewPanel op)\r
- {\r
- overviewPanel = op;\r
- }\r
-\r
- public void setAnnotationVisible(boolean b)\r
- {\r
- if (!av.wrapAlignment)\r
- {\r
- annotationSpaceFillerHolder.setVisible(b);\r
- annotationPanel.setVisible(b);\r
- }\r
- validate();\r
- repaint();\r
- }\r
-\r
- public void setWrapAlignment(boolean wrap)\r
- {\r
- av.startSeq = 0;\r
- av.startRes = 0;\r
- scalePanelHolder.setVisible(!wrap);\r
-\r
- hscroll.setVisible(!wrap);\r
- idwidthAdjuster.setVisible(!wrap);\r
-\r
- if (wrap)\r
- {\r
- annotationPanel.setVisible(false);\r
- annotationSpaceFillerHolder.setVisible(false);\r
- }\r
- else if (av.showAnnotation)\r
- {\r
- annotationPanel.setVisible(true);\r
- annotationSpaceFillerHolder.setVisible(true);\r
- }\r
-\r
- idSpaceFillerPanel1.setVisible(!wrap);\r
-\r
- fontChanged(); //This is so that the scalePanel is resized correctly\r
-\r
- validate();\r
- repaint();\r
-\r
- }\r
-\r
- int hextent = 0;\r
- int vextent = 0;\r
-\r
- // return value is true if the scroll is valid\r
- public boolean scrollUp(boolean up)\r
- {\r
- if (up)\r
- {\r
- if (vscroll.getValue() < 1)\r
- {\r
- return false;\r
- }\r
- setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);\r
- }\r
- else\r
- {\r
- if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())\r
- {\r
- return false;\r
- }\r
- setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);\r
- }\r
-\r
- repaint();\r
- return true;\r
- }\r
-\r
- public boolean scrollRight(boolean right)\r
- {\r
- if (!right)\r
- {\r
- if (hscroll.getValue() < 1)\r
- {\r
- return false;\r
- }\r
- setScrollValues(hscroll.getValue() - 1, vscroll.getValue());\r
- }\r
- else\r
- {\r
- if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())\r
- {\r
- return false;\r
- }\r
- setScrollValues(hscroll.getValue() + 1, vscroll.getValue());\r
- }\r
-\r
- repaint();\r
- return true;\r
- }\r
-\r
- public void setScrollValues(int x, int y)\r
- {\r
- int width = av.alignment.getWidth();\r
- int height = av.alignment.getHeight();\r
-\r
- if (av.hasHiddenColumns)\r
- {\r
- width = av.getColumnSelection().findColumnPosition(width);\r
- }\r
-\r
- av.setStartRes(x);\r
- av.setEndRes( (x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);\r
-\r
- hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;\r
- vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;\r
-\r
- if (hextent > width)\r
- {\r
- hextent = width;\r
- }\r
-\r
- if (vextent > height)\r
- {\r
- vextent = height;\r
- }\r
-\r
- if ( (hextent + x) > width)\r
- {\r
- x = width - hextent;\r
- }\r
-\r
- if ( (vextent + y) > height)\r
- {\r
- y = height - vextent;\r
- }\r
-\r
- if (y < 0)\r
- {\r
- y = 0;\r
- }\r
-\r
- if (x < 0)\r
- {\r
- x = 0;\r
- }\r
-\r
- av.setStartSeq(y);\r
-\r
- int endSeq = y + vextent;\r
- if (endSeq > av.alignment.getHeight())\r
- {\r
- endSeq = av.alignment.getHeight();\r
- }\r
-\r
- av.setEndSeq(endSeq);\r
- hscroll.setValues(x, hextent, 0, width);\r
- vscroll.setValues(y, vextent, 0, height);\r
-\r
- if (overviewPanel != null)\r
- {\r
- overviewPanel.setBoxPosition();\r
- }\r
-\r
- }\r
-\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
- {\r
- int oldX = av.getStartRes();\r
- int oldY = av.getStartSeq();\r
-\r
- if (evt == null || evt.getSource() == hscroll)\r
- {\r
- int x = hscroll.getValue();\r
- av.setStartRes(x);\r
- av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() -\r
- 1);\r
- }\r
-\r
- if (evt == null || evt.getSource() == vscroll)\r
- {\r
- int offy = vscroll.getValue();\r
- if (av.getWrapAlignment())\r
- {\r
- int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.\r
- seqCanvas.getSize().width);\r
- av.setStartRes(vscroll.getValue() * rowSize);\r
- av.setEndRes( (vscroll.getValue() + 1) * rowSize);\r
- }\r
- else\r
- {\r
- av.setStartSeq(offy);\r
- av.setEndSeq(offy +\r
- seqPanel.seqCanvas.getSize().height / av.getCharHeight());\r
- }\r
- }\r
-\r
- if (overviewPanel != null)\r
- {\r
- overviewPanel.setBoxPosition();\r
- }\r
-\r
- int scrollX = av.startRes - oldX;\r
- int scrollY = av.startSeq - oldY;\r
-\r
- if (av.getWrapAlignment() || !fastPaint || av.MAC)\r
- {\r
- repaint();\r
- }\r
- else\r
- {\r
- // Make sure we're not trying to draw a panel\r
- // larger than the visible window\r
- if (scrollX > av.endRes - av.startRes)\r
- {\r
- scrollX = av.endRes - av.startRes;\r
- }\r
- else if (scrollX < av.startRes - av.endRes)\r
- {\r
- scrollX = av.startRes - av.endRes;\r
- }\r
-\r
- idPanel.idCanvas.fastPaint(scrollY);\r
- seqPanel.seqCanvas.fastPaint(scrollX,\r
- scrollY);\r
-\r
- scalePanel.repaint();\r
- if (av.getShowAnnotation())\r
- {\r
- annotationPanel.fastPaint(av.getStartRes() - oldX);\r
- }\r
- }\r
-\r
- }\r
-\r
- public void paintAlignment(boolean updateOverview)\r
- {\r
- repaint();\r
-\r
- if(updateOverview)\r
- {\r
- jalview.structure.StructureSelectionManager.getStructureSelectionManager()\r
- .sequenceColoursChanged(this);\r
-\r
- if (overviewPanel != null)\r
- {\r
- overviewPanel.updateOverviewImage();\r
- }\r
- }\r
- }\r
-\r
- public void update(Graphics g)\r
- {\r
- paint(g);\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\r
- invalidate();\r
- Dimension d = idPanel.idCanvas.getSize();\r
- idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);\r
- annotationSpaceFillerHolder.setSize(d.width,\r
- annotationPanel.getSize().height);\r
-\r
- alabels.setSize(d.width, annotationPanel.getSize().height);\r
-\r
- if (av.getWrapAlignment())\r
- {\r
- int maxwidth = av.alignment.getWidth();\r
-\r
- if (av.hasHiddenColumns)\r
- {\r
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
- }\r
-\r
- int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth\r
- (seqPanel.seqCanvas.getSize().width);\r
-\r
- if (canvasWidth > 0)\r
- {\r
- int max = maxwidth / canvasWidth;\r
- vscroll.setMaximum(max);\r
- vscroll.setUnitIncrement(1);\r
- vscroll.setVisibleAmount(1);\r
- }\r
- }\r
- else\r
- {\r
- setScrollValues(av.getStartRes(), av.getStartSeq());\r
- }\r
-\r
- alabels.repaint();\r
-\r
- seqPanel.seqCanvas.repaint();\r
- scalePanel.repaint();\r
- annotationPanel.repaint();\r
- idPanel.idCanvas.repaint();\r
- }\r
-\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
- BorderLayout borderLayout4 = new BorderLayout();\r
- BorderLayout borderLayout2 = new BorderLayout();\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\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
- sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);\r
- sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);\r
- seqPanelHolder.add(vscroll, BorderLayout.EAST);\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
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.JalviewLite;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.beans.PropertyChangeEvent;
+import java.util.List;
+
+public class AlignmentPanel extends Panel
+ implements AdjustmentListener, AlignmentViewPanel, ViewportListenerI
+{
+
+ public AlignViewport av;
+
+ OverviewPanel overviewPanel;
+
+ SeqPanel seqPanel;
+
+ IdPanel idPanel;
+
+ IdwidthAdjuster idwidthAdjuster;
+
+ public AlignFrame alignFrame;
+
+ ScalePanel scalePanel;
+
+ AnnotationPanel annotationPanel;
+
+ AnnotationLabels alabels;
+
+ ViewportRanges vpRanges;
+
+ // this value is set false when selection area being dragged
+ boolean fastPaint = true;
+
+ public AlignmentPanel(AlignFrame af, final AlignViewport av)
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ alignFrame = af;
+ this.av = av;
+ vpRanges = av.getRanges();
+ seqPanel = new SeqPanel(av, this);
+ idPanel = new IdPanel(av, this);
+ scalePanel = new ScalePanel(av, this);
+ idwidthAdjuster = new IdwidthAdjuster(this);
+ annotationPanel = new AnnotationPanel(this);
+ annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
+
+ sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
+ alabels = new AnnotationLabels(this);
+
+ setAnnotationVisible(av.isShowAnnotation());
+
+ idPanelHolder.add(idPanel, BorderLayout.CENTER);
+ idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
+ annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
+ scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
+ seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
+
+ fontChanged();
+ setScrollValues(0, 0);
+
+ apvscroll.addAdjustmentListener(this);
+ hscroll.addAdjustmentListener(this);
+ vscroll.addAdjustmentListener(this);
+
+ addComponentListener(new ComponentAdapter()
+ {
+ @Override
+ public void componentResized(ComponentEvent evt)
+ {
+ // reset the viewport ranges when the alignment panel is resized
+ // in particular, this initialises the end residue value when Jalview
+ // is initialised
+ if (av.getWrapAlignment())
+ {
+ int widthInRes = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+ vpRanges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = seqPanel.seqCanvas.getWidth()
+ / av.getCharWidth();
+ int heightInSeq = seqPanel.seqCanvas.getHeight()
+ / av.getCharHeight();
+
+ vpRanges.setViewportWidth(widthInRes);
+ vpRanges.setViewportHeight(heightInSeq);
+ }
+ // setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
+ if (getSize().height > 0
+ && annotationPanelHolder.getSize().height > 0)
+ {
+ validateAnnotationDimensions(false);
+ }
+ repaint();
+ }
+
+ });
+
+ Dimension d = calculateIdWidth();
+ idPanel.idCanvas.setSize(d);
+
+ hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height);
+
+ idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
+ annotationSpaceFillerHolder.setSize(d.width,
+ annotationPanel.getSize().height);
+ alabels.setSize(d.width, annotationPanel.getSize().height);
+ final AlignmentPanel ap = this;
+ av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
+ {
+ @Override
+ public void propertyChange(java.beans.PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment"))
+ {
+ PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
+ alignmentChanged();
+ }
+ }
+ });
+ av.getRanges().addPropertyChangeListener(this);
+ }
+
+ @Override
+ public AlignViewportI getAlignViewport()
+ {
+ return av;
+ }
+
+ public SequenceRenderer getSequenceRenderer()
+ {
+ return seqPanel.seqCanvas.sr;
+ }
+
+ @Override
+ public jalview.api.FeatureRenderer getFeatureRenderer()
+ {
+ return seqPanel.seqCanvas.fr;
+ }
+
+ @Override
+ public jalview.api.FeatureRenderer cloneFeatureRenderer()
+ {
+ FeatureRenderer nfr = new FeatureRenderer(av);
+ nfr.transferSettings(seqPanel.seqCanvas.fr);
+ return nfr;
+ }
+
+ public void alignmentChanged()
+ {
+ av.alignmentChanged(this);
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.updateOverviewImage();
+ }
+
+ alignFrame.updateEditMenuBar();
+
+ repaint();
+ }
+
+ public void fontChanged()
+ {
+ // set idCanvas bufferedImage to null
+ // to prevent drawing old image
+ idPanel.idCanvas.image = null;
+ FontMetrics fm = getFontMetrics(av.getFont());
+
+ scalePanel.setSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
+ idwidthAdjuster.setSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
+ av.updateSequenceIdColours();
+ annotationPanel.image = null;
+ int ap = annotationPanel.adjustPanelHeight(false);
+ Dimension d = calculateIdWidth();
+ d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
+ alabels.setSize(d.width + 4, ap);
+
+ idPanel.idCanvas.setSize(d);
+ hscrollFillerPanel.setSize(d);
+
+ validateAnnotationDimensions(false);
+ annotationPanel.repaint();
+ validate();
+ repaint();
+ }
+
+ public void setIdWidth(int w, int h)
+ {
+ idPanel.idCanvas.setSize(w, h);
+ idPanelHolder.setSize(w, idPanelHolder.getSize().height);
+ annotationSpaceFillerHolder.setSize(w,
+ annotationSpaceFillerHolder.getSize().height);
+ alabels.setSize(w, alabels.getSize().height);
+ validate();
+ }
+
+ Dimension calculateIdWidth()
+ {
+ if (av.nullFrame == null)
+ {
+ av.nullFrame = new Frame();
+ av.nullFrame.addNotify();
+ }
+
+ Graphics g = av.nullFrame.getGraphics();
+
+ FontMetrics fm = g.getFontMetrics(av.font);
+ AlignmentI al = av.getAlignment();
+
+ int i = 0;
+ int idWidth = 0;
+ String id;
+ while (i < al.getHeight() && al.getSequenceAt(i) != null)
+ {
+ SequenceI s = al.getSequenceAt(i);
+ id = s.getDisplayId(av.getShowJVSuffix());
+
+ if (fm.stringWidth(id) > idWidth)
+ {
+ idWidth = fm.stringWidth(id);
+ }
+ i++;
+ }
+
+ // Also check annotation label widths
+ i = 0;
+ if (al.getAlignmentAnnotation() != null)
+ {
+ fm = g.getFontMetrics(av.nullFrame.getFont());
+ while (i < al.getAlignmentAnnotation().length)
+ {
+ String label = al.getAlignmentAnnotation()[i].label;
+ if (fm.stringWidth(label) > idWidth)
+ {
+ idWidth = fm.stringWidth(label);
+ }
+ i++;
+ }
+ }
+
+ return new Dimension(idWidth, idPanel.idCanvas.getSize().height);
+ }
+
+ /**
+ * Highlight the given results on the alignment.
+ *
+ */
+ public void highlightSearchResults(SearchResultsI results)
+ {
+ scrollToPosition(results);
+ seqPanel.seqCanvas.highlightSearchResults(results);
+ }
+
+ /**
+ * scroll the view to show the position of the highlighted region in results
+ * (if any) and redraw the overview
+ *
+ * @param results
+ * @return false if results were not found
+ */
+ public boolean scrollToPosition(SearchResultsI results)
+ {
+ return scrollToPosition(results, true);
+ }
+
+ /**
+ * scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
+ * @param results
+ * @param redrawOverview
+ * - when set, the overview will be recalculated (takes longer)
+ * @return false if results were not found
+ */
+ public boolean scrollToPosition(SearchResultsI results,
+ boolean redrawOverview)
+ {
+ return scrollToPosition(results, 0, redrawOverview, false);
+ }
+
+ /**
+ * scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
+ * @param results
+ * @param redrawOverview
+ * - when set, the overview will be recalculated (takes longer)
+ * @return false if results were not found
+ */
+ public boolean scrollToPosition(SearchResultsI results,
+ int verticalOffset, boolean redrawOverview, boolean centre)
+ {
+ // do we need to scroll the panel?
+ if (results != null && results.getCount() > 0)
+ {
+ AlignmentI alignment = av.getAlignment();
+ int seqIndex = alignment.findIndex(results);
+ if (seqIndex == -1)
+ {
+ return false;
+ }
+ /*
+ * allow for offset of target sequence (actually scroll to one above it)
+ */
+
+ SequenceI seq = alignment.getSequenceAt(seqIndex);
+ int[] r = results.getResults(seq, 0, alignment.getWidth());
+ if (r == null)
+ {
+ if (JalviewLite.debug)
+ {// DEBUG
+ System.out.println(
+ "DEBUG: scroll didn't happen - results not within alignment : "
+ + seq.getStart() + "," + seq.getEnd());
+ }
+ return false;
+ }
+ if (JalviewLite.debug)
+ {
+ // DEBUG
+ /*
+ * System.out.println("DEBUG: scroll: start=" + r[0] +
+ * " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] +
+ * " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() +
+ * " hextent=" + hextent);
+ */
+ }
+ int start = r[0];
+ int end = r[1];
+
+ /*
+ * To centre results, scroll to positions half the visible width
+ * left/right of the start/end positions
+ */
+ if (centre)
+ {
+ int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2
+ - 1;
+ start = Math.max(start - offset, 0);
+ end = end + offset - 1;
+ // end = Math.min(end + offset, seq.getEnd() - 1);
+ }
+
+ if (start < 0)
+ {
+ return false;
+ }
+ if (end == seq.getEnd())
+ {
+ return false;
+ }
+
+ /*
+ * allow for offset of target sequence (actually scroll to one above it)
+ */
+ seqIndex = Math.max(0, seqIndex - verticalOffset);
+ return scrollTo(start, end, seqIndex, false, redrawOverview);
+ }
+ return true;
+ }
+
+ public boolean scrollTo(int ostart, int end, int seqIndex,
+ boolean scrollToNearest, boolean redrawOverview)
+ {
+ int startv, endv, starts, ends, width;
+
+ int start = -1;
+ if (av.hasHiddenColumns())
+ {
+ AlignmentI al = av.getAlignment();
+ start = al.getHiddenColumns().absoluteToVisibleColumn(ostart);
+ end = al.getHiddenColumns().absoluteToVisibleColumn(end);
+ if (start == end)
+ {
+ if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart))
+ {
+ // don't scroll - position isn't visible
+ return false;
+ }
+ }
+ }
+ else
+ {
+ start = ostart;
+ }
+
+ if (!av.getWrapAlignment())
+ {
+ /*
+ * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
+ * av.getStartRes()) >= start) { spos=start-1; // seqIn //
+ * setScrollValues(start - 1, seqIndex); } else if ((endv =
+ * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
+ * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
+ * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
+ * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
+ * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
+ */
+
+ // below is scrolling logic up to Jalview 2.8.2
+ // if ((av.getStartRes() > end)
+ // || (av.getEndRes() < start)
+ // || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+ // {
+ // if (start > av.getAlignment().getWidth() - hextent)
+ // {
+ // start = av.getAlignment().getWidth() - hextent;
+ // if (start < 0)
+ // {
+ // start = 0;
+ // }
+ //
+ // }
+ // if (seqIndex > av.getAlignment().getHeight() - vextent)
+ // {
+ // seqIndex = av.getAlignment().getHeight() - vextent;
+ // if (seqIndex < 0)
+ // {
+ // seqIndex = 0;
+ // }
+ // }
+ // setScrollValues(start, seqIndex);
+ // }
+ // logic copied from jalview.gui.AlignmentPanel:
+ if ((startv = vpRanges.getStartRes()) >= start)
+ {
+ /*
+ * Scroll left to make start of search results visible
+ */
+ setScrollValues(start - 1, seqIndex);
+ }
+ else if ((endv = vpRanges.getEndRes()) <= end)
+ {
+ /*
+ * Scroll right to make end of search results visible
+ */
+ setScrollValues(startv + 1 + end - endv, seqIndex);
+ }
+ else if ((starts = vpRanges.getStartSeq()) > seqIndex)
+ {
+ /*
+ * Scroll up to make start of search results visible
+ */
+ setScrollValues(vpRanges.getStartRes(), seqIndex);
+ }
+ else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
+ {
+ /*
+ * Scroll down to make end of search results visible
+ */
+ setScrollValues(vpRanges.getStartRes(),
+ starts + seqIndex - ends + 1);
+ }
+ /*
+ * Else results are already visible - no need to scroll
+ */
+ }
+ else
+ {
+ vpRanges.scrollToWrappedVisible(start);
+ }
+
+ paintAlignment(redrawOverview, false);
+ return true;
+ }
+
+ public OverviewPanel getOverviewPanel()
+ {
+ return overviewPanel;
+ }
+
+ public void setOverviewPanel(OverviewPanel op)
+ {
+ overviewPanel = op;
+ }
+
+ public void setAnnotationVisible(boolean b)
+ {
+ if (!av.getWrapAlignment())
+ {
+ annotationSpaceFillerHolder.setVisible(b);
+ annotationPanelHolder.setVisible(b);
+ }
+ else
+ {
+ annotationSpaceFillerHolder.setVisible(false);
+ annotationPanelHolder.setVisible(false);
+ }
+ validate();
+ repaint();
+ }
+
+ /**
+ * automatically adjust annotation panel height for new annotation whilst
+ * ensuring the alignment is still visible.
+ */
+ @Override
+ public void adjustAnnotationHeight()
+ {
+ // TODO: display vertical annotation scrollbar if necessary
+ // this is called after loading new annotation onto alignment
+ if (alignFrame.getSize().height == 0)
+ {
+ System.out.println(
+ "adjustAnnotationHeight frame size zero NEEDS FIXING");
+ }
+ fontChanged();
+ validateAnnotationDimensions(true);
+ apvscroll.addNotify();
+ hscroll.addNotify();
+ validate();
+ paintAlignment(true, false);
+ }
+
+ /**
+ * Calculate the annotation dimensions and refresh slider values accordingly.
+ * Need to do repaints/notifys afterwards.
+ */
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight)
+ {
+ int rowHeight = av.getCharHeight();
+ int alignmentHeight = rowHeight * av.getAlignment().getHeight();
+ int annotationHeight = av.calcPanelHeight();
+
+ int mheight = annotationHeight;
+ Dimension d = sequenceHolderPanel.getSize();
+
+ int availableHeight = d.height - scalePanelHolder.getHeight();
+
+ if (adjustPanelHeight)
+ {
+ /*
+ * If not enough vertical space, maximize annotation height while keeping
+ * at least two rows of alignment visible
+ */
+ if (annotationHeight + alignmentHeight > availableHeight)
+ {
+ annotationHeight = Math.min(annotationHeight,
+ availableHeight - 2 * rowHeight);
+ }
+ }
+ else
+ {
+ // maintain same window layout whilst updating sliders
+ annotationHeight = annotationPanelHolder.getSize().height;
+ }
+
+ if (availableHeight - annotationHeight < 5)
+ {
+ annotationHeight = availableHeight;
+ }
+
+ annotationPanel.setSize(new Dimension(d.width, annotationHeight));
+ annotationPanelHolder.setSize(new Dimension(d.width, annotationHeight));
+ // seqPanelHolder.setSize(d.width, seqandannot - height);
+ seqPanel.seqCanvas.setSize(d.width,
+ seqPanel.seqCanvas.getSize().height);
+
+ Dimension e = idPanel.getSize();
+ alabels.setSize(new Dimension(e.width, annotationHeight));
+ annotationSpaceFillerHolder
+ .setSize(new Dimension(e.width, annotationHeight));
+
+ int s = apvscroll.getValue();
+ if (s > mheight - annotationHeight)
+ {
+ s = 0;
+ }
+ apvscroll.setValues(s, annotationHeight, 0, mheight);
+ annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+ alabels.setScrollOffset(apvscroll.getValue(), false);
+ }
+
+ public void setWrapAlignment(boolean wrap)
+ {
+ vpRanges.setStartEndSeq(0, vpRanges.getVisibleAlignmentHeight());
+ vpRanges.setStartRes(0);
+ scalePanelHolder.setVisible(!wrap);
+
+ hscroll.setVisible(!wrap);
+ idwidthAdjuster.setVisible(!wrap);
+
+ if (wrap)
+ {
+ annotationPanelHolder.setVisible(false);
+ annotationSpaceFillerHolder.setVisible(false);
+ }
+ else if (av.isShowAnnotation())
+ {
+ annotationPanelHolder.setVisible(true);
+ annotationSpaceFillerHolder.setVisible(true);
+ }
+
+ idSpaceFillerPanel1.setVisible(!wrap);
+
+ fontChanged(); // This is so that the scalePanel is resized correctly
+
+ validate();
+ sequenceHolderPanel.validate();
+ repaint();
+
+ }
+
+ int hextent = 0;
+
+ int vextent = 0;
+
+ public void setScrollValues(int xpos, int ypos)
+ {
+ int x = xpos;
+ int y = ypos;
+
+ if (av.getWrapAlignment())
+ {
+ setScrollingForWrappedPanel(x);
+ }
+ else
+ {
+ int width = av.getAlignment().getVisibleWidth();
+ int height = av.getAlignment().getHeight();
+
+ if (x < 0)
+ {
+ x = 0;
+ }
+
+ hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
+ vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
+
+ if (hextent > width)
+ {
+ hextent = width;
+ }
+
+ if (vextent > height)
+ {
+ vextent = height;
+ }
+
+ if ((hextent + x) > width)
+ {
+ System.err.println("hextent was " + hextent + " and x was " + x);
+
+ x = width - hextent;
+ }
+
+ if ((vextent + y) > height)
+ {
+ y = height - vextent;
+ }
+
+ if (y < 0)
+ {
+ y = 0;
+ }
+
+ if (x < 0)
+ {
+ System.err.println("x was " + x);
+ x = 0;
+ }
+
+ hscroll.setValues(x, hextent, 0, width);
+ vscroll.setValues(y, vextent, 0, height);
+
+ // AWT scrollbar does not fire adjustmentValueChanged for setValues
+ // so also call adjustment code!
+ adjustHorizontal(x);
+ adjustVertical(y);
+
+ sendViewPosition();
+ }
+ }
+
+ /**
+ * Respond to adjustment event when horizontal or vertical scrollbar is
+ * changed
+ *
+ * @param evt
+ * adjustment event encoding whether apvscroll, hscroll or vscroll
+ * changed
+ */
+ @Override
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ // Note that this event is NOT fired by the AWT scrollbar when setValues is
+ // called. Instead manually call adjustHorizontal and adjustVertical
+ // directly.
+ if (evt == null || evt.getSource() == apvscroll)
+ {
+ annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+ alabels.setScrollOffset(apvscroll.getValue(), false);
+ }
+ if (evt == null || evt.getSource() == hscroll)
+ {
+ int x = hscroll.getValue();
+ adjustHorizontal(x);
+ }
+
+ if (evt == null || evt.getSource() == vscroll)
+ {
+ int offy = vscroll.getValue();
+ adjustVertical(offy);
+ }
+
+ }
+
+ private void adjustHorizontal(int x)
+ {
+ int oldX = vpRanges.getStartRes();
+ int oldwidth = vpRanges.getViewportWidth();
+ int width = seqPanel.seqCanvas.getWidth() / av.getCharWidth();
+
+ // if we're scrolling to the position we're already at, stop
+ // this prevents infinite recursion of events when the scroll/viewport
+ // ranges values are the same
+ if ((x == oldX) && (width == oldwidth))
+ {
+ return;
+ }
+ vpRanges.setViewportStartAndWidth(x, width);
+
+ if (av.getWrapAlignment() || !fastPaint)
+ {
+ repaint();
+ }
+ sendViewPosition();
+ }
+
+ private void adjustVertical(int newY)
+ {
+ if (av.getWrapAlignment())
+ {
+ /*
+ * if we're scrolling to the position we're already at, stop
+ * this prevents infinite recursion of events when the scroll/viewport
+ * ranges values are the same
+ */
+ int oldX = vpRanges.getStartRes();
+ int oldY = vpRanges.getWrappedScrollPosition(oldX);
+ if (oldY == newY)
+ {
+ return;
+ }
+ if (newY > -1)
+ {
+ /*
+ * limit page up/down to one width's worth of positions
+ */
+ int rowSize = vpRanges.getViewportWidth();
+ int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
+ vpRanges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
+ }
+ }
+ else
+ {
+ int height = seqPanel.seqCanvas.getHeight() / av.getCharHeight();
+ int oldY = vpRanges.getStartSeq();
+ int oldheight = vpRanges.getViewportHeight();
+
+ // if we're scrolling to the position we're already at, stop
+ // this prevents infinite recursion of events when the scroll/viewport
+ // ranges values are the same
+ if ((newY == oldY) && (height == oldheight))
+ {
+ return;
+ }
+ vpRanges.setViewportStartAndHeight(newY, height);
+ }
+ if (av.getWrapAlignment() || !fastPaint)
+ {
+ repaint();
+ }
+ sendViewPosition();
+ }
+
+ /**
+ * A helper method to return the AlignmentPanel in the other (complementary)
+ * half of a SplitFrame view. Returns null if not in a SplitFrame.
+ *
+ * @return
+ */
+ private AlignmentPanel getComplementPanel()
+ {
+ AlignmentPanel ap = null;
+ if (alignFrame != null)
+ {
+ SplitFrame sf = alignFrame.getSplitFrame();
+ if (sf != null)
+ {
+ AlignFrame other = sf.getComplement(alignFrame);
+ if (other != null)
+ {
+ ap = other.alignPanel;
+ }
+ }
+ }
+ return ap;
+ }
+
+ /**
+ * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
+ * The aim is to keep the two alignments 'lined up' on their centre columns.
+ *
+ * @param sr
+ * holds mapped region(s) of this alignment that we are scrolling
+ * 'to'; may be modified for sequence offset by this method
+ * @param seqOffset
+ * the number of visible sequences to show above the mapped region
+ */
+ protected void scrollToCentre(SearchResultsI sr, int seqOffset)
+ {
+ /*
+ * To avoid jumpy vertical scrolling (if some sequences are gapped or not
+ * mapped), we can make the scroll-to location a sequence above the one
+ * actually mapped.
+ */
+ SequenceI mappedTo = sr.getResults().get(0).getSequence();
+ List<SequenceI> seqs = av.getAlignment().getSequences();
+
+ /*
+ * This is like AlignmentI.findIndex(seq) but here we are matching the
+ * dataset sequence not the aligned sequence
+ */
+ boolean matched = false;
+ for (SequenceI seq : seqs)
+ {
+ if (mappedTo == seq.getDatasetSequence())
+ {
+ matched = true;
+ break;
+ }
+ }
+ if (!matched)
+ {
+ return; // failsafe, shouldn't happen
+ }
+
+ /*
+ * Scroll to position but centring the target residue. Also set a state flag
+ * to prevent adjustmentValueChanged performing this recursively.
+ */
+ scrollToPosition(sr, seqOffset, true, true);
+ }
+
+ private void sendViewPosition()
+ {
+ StructureSelectionManager.getStructureSelectionManager(av.applet)
+ .sendViewPosition(this, vpRanges.getStartRes(),
+ vpRanges.getEndRes(), vpRanges.getStartSeq(),
+ vpRanges.getEndSeq());
+ }
+
+ /**
+ * Repaint the alignment and annotations, and, optionally, any overview window
+ */
+ @Override
+ public void paintAlignment(boolean updateOverview,
+ boolean updateStructures)
+ {
+ final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+ av.isShowAutocalculatedAbove());
+ sorter.sort(getAlignment().getAlignmentAnnotation(),
+ av.getSortAnnotationsBy());
+ repaint();
+
+ if (updateStructures)
+ {
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(av.applet)
+ .sequenceColoursChanged(this);
+ }
+ if (updateOverview)
+ {
+ if (overviewPanel != null)
+ {
+ overviewPanel.updateOverviewImage();
+ }
+ }
+ }
+
+ @Override
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
+
+ @Override
+ public void paint(Graphics g)
+ {
+ invalidate();
+ Dimension d = idPanel.idCanvas.getSize();
+ final int canvasHeight = seqPanel.seqCanvas.getSize().height;
+ if (canvasHeight != d.height)
+ {
+ idPanel.idCanvas.setSize(d.width, canvasHeight);
+ }
+
+ setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
+
+ seqPanel.seqCanvas.repaint();
+ idPanel.idCanvas.repaint();
+ if (!av.getWrapAlignment())
+ {
+ if (av.isShowAnnotation())
+ {
+ alabels.repaint();
+ annotationPanel.repaint();
+ }
+ scalePanel.repaint();
+ }
+
+ }
+
+ /**
+ * Set vertical scroll bar parameters for wrapped panel
+ *
+ * @param topLeftColumn
+ * the column position at top left (0..)
+ */
+ private void setScrollingForWrappedPanel(int topLeftColumn)
+ {
+ int scrollPosition = vpRanges.getWrappedScrollPosition(topLeftColumn);
+ int maxScroll = vpRanges.getWrappedMaxScroll(topLeftColumn);
+
+ /*
+ * a scrollbar's value can be set to at most (maximum-extent)
+ * so we add extent (1) to the maxScroll value
+ */
+ vscroll.setUnitIncrement(1);
+ vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
+ }
+
+ protected Panel sequenceHolderPanel = new Panel();
+
+ protected Scrollbar vscroll = new Scrollbar();
+
+ protected Scrollbar hscroll = new Scrollbar();
+
+ protected Panel seqPanelHolder = new Panel();
+
+ protected Panel scalePanelHolder = new Panel();
+
+ protected Panel idPanelHolder = new Panel();
+
+ protected Panel idSpaceFillerPanel1 = new Panel();
+
+ public Panel annotationSpaceFillerHolder = new Panel();
+
+ protected Panel hscrollFillerPanel = new Panel();
+
+ Panel annotationPanelHolder = new Panel();
+
+ protected Scrollbar apvscroll = new Scrollbar();
+
+ /*
+ * Flag set while scrolling to follow complementary cDNA/protein scroll. When
+ * false, suppresses invoking the same method recursively.
+ */
+ private boolean scrollComplementaryPanel = true;
+
+ private void jbInit() throws Exception
+ {
+ // idPanelHolder.setPreferredSize(new Dimension(70, 10));
+ this.setLayout(new BorderLayout());
+
+ // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
+ sequenceHolderPanel.setLayout(new BorderLayout());
+ seqPanelHolder.setLayout(new BorderLayout());
+ scalePanelHolder.setBackground(Color.white);
+
+ // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
+ scalePanelHolder.setLayout(new BorderLayout());
+ idPanelHolder.setLayout(new BorderLayout());
+ idSpaceFillerPanel1.setBackground(Color.white);
+
+ // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
+ idSpaceFillerPanel1.setLayout(new BorderLayout());
+ annotationSpaceFillerHolder.setBackground(Color.white);
+
+ // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
+ annotationSpaceFillerHolder.setLayout(new BorderLayout());
+ hscroll.setOrientation(Scrollbar.HORIZONTAL);
+
+ Panel hscrollHolder = new Panel();
+ hscrollHolder.setLayout(new BorderLayout());
+ hscrollFillerPanel.setBackground(Color.white);
+ apvscroll.setOrientation(Scrollbar.VERTICAL);
+ apvscroll.setVisible(true);
+ apvscroll.addAdjustmentListener(this);
+
+ annotationPanelHolder.setBackground(Color.white);
+ annotationPanelHolder.setLayout(new BorderLayout());
+ annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
+ // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
+ hscrollHolder.setBackground(Color.white);
+
+ // annotationScroller.setPreferredSize(new Dimension(10, 80));
+ // this.setPreferredSize(new Dimension(220, 166));
+ seqPanelHolder.setBackground(Color.white);
+ idPanelHolder.setBackground(Color.white);
+ sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH);
+ sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER);
+ seqPanelHolder.add(vscroll, BorderLayout.EAST);
+
+ // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH);
+ this.add(idPanelHolder, BorderLayout.WEST);
+ idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH);
+ idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH);
+ this.add(hscrollHolder, BorderLayout.SOUTH);
+ hscrollHolder.add(hscroll, BorderLayout.CENTER);
+ hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST);
+ this.add(sequenceHolderPanel, BorderLayout.CENTER);
+ }
+
+ /**
+ * hides or shows dynamic annotation rows based on groups and av state flags
+ */
+ public void updateAnnotation()
+ {
+ updateAnnotation(false);
+ }
+
+ public void updateAnnotation(boolean applyGlobalSettings)
+ {
+ updateAnnotation(applyGlobalSettings, false);
+ }
+
+ public void updateAnnotation(boolean applyGlobalSettings,
+ boolean preserveNewGroupSettings)
+ {
+ av.updateGroupAnnotationSettings(applyGlobalSettings,
+ preserveNewGroupSettings);
+ adjustAnnotationHeight();
+ }
+
+ @Override
+ public AlignmentI getAlignment()
+ {
+ return av.getAlignment();
+ }
+
+ @Override
+ public String getViewName()
+ {
+ return getName();
+ }
+
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager
+ .getStructureSelectionManager(av.applet);
+ }
+
+ @Override
+ public void raiseOOMWarning(String string, OutOfMemoryError error)
+ {
+ // TODO: JAL-960
+ System.err.println("Out of memory whilst '" + string + "'");
+ error.printStackTrace();
+ }
+
+ /**
+ * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
+ *
+ * @param b
+ */
+ protected void setToScrollComplementPanel(boolean b)
+ {
+ this.scrollComplementaryPanel = b;
+ }
+
+ /**
+ * Get whether to scroll complement panel
+ *
+ * @return true if cDNA/protein complement panels should be scrolled
+ */
+ protected boolean isSetToScrollComplementPanel()
+ {
+ return this.scrollComplementaryPanel;
+ }
+
+ @Override
+ /**
+ * Property change event fired when a change is made to the viewport ranges
+ * object associated with this alignment panel's viewport
+ */
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // update this panel's scroll values based on the new viewport ranges values
+ int x = vpRanges.getStartRes();
+ int y = vpRanges.getStartSeq();
+ setScrollValues(x, y);
+
+ // now update any complementary alignment (its viewport ranges object
+ // is different so does not get automatically updated)
+ if (isSetToScrollComplementPanel())
+ {
+ setToScrollComplementPanel(false);
+ av.scrollComplementaryAlignment(getComplementPanel());
+ setToScrollComplementPanel(true);
+ }
+
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff