-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 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 extends Panel implements AdjustmentListener\r
-{\r
-\r
- 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
-\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
-\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
-\r
- public void alignmentChanged()\r
- {\r
- av.alignmentChanged(this);\r
-\r
- if (overviewPanel != null)\r
- overviewPanel.updateOverviewImage();\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
- overviewPanel.updateOverviewImage();\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
- start = 0;\r
- }\r
- if (seqIndex > av.alignment.getHeight() - vextent)\r
- {\r
- seqIndex = av.alignment.getHeight() - vextent;\r
- if (seqIndex < 0)\r
- seqIndex = 0;\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.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
-\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
- scalePanelHolder.setVisible(!wrap);\r
-\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
-\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
-\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
- width = av.getColumnSelection().findColumnPosition(width);\r
-\r
- av.setStartRes(x);\r
- av.setStartSeq(y);\r
-\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
- 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, av.getAlignment().getWidth());\r
- vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());\r
-\r
- if(overviewPanel!=null)\r
- overviewPanel.setBoxPosition();\r
-\r
- }\r
-\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
- {\r
- int oldX = av.getStartRes();\r
- int oldY = av.getStartSeq();\r
-\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
-\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
- scrollX = av.startRes - av.endRes;\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 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
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\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
- if (getBounds() == g.getClipBounds())\r
- {\r
- if (overviewPanel != null)\r
- overviewPanel.updateOverviewImage();\r
- }\r
-\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() 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
- 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.*;
+import jalview.structure.StructureSelectionManager;
+
+public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel
+{
+
+ public AlignViewport av;
+
+ OverviewPanel overviewPanel;
+
+ SeqPanel seqPanel;
+
+ IdPanel idPanel;
+
+ IdwidthAdjuster idwidthAdjuster;
+
+ public AlignFrame alignFrame;
+
+ ScalePanel scalePanel;
+
+ AnnotationPanel annotationPanel;
+
+ AnnotationLabels alabels;
+
+ // this value is set false when selection area being dragged
+ boolean fastPaint = true;
+
+ public void finalize() {
+ alignFrame=null;
+ av=null;
+ seqPanel=null;
+ seqPanelHolder=null;
+ sequenceHolderPanel=null;
+ scalePanel=null;
+ scalePanelHolder=null;
+ annotationPanel=null;
+ annotationPanelHolder=null;
+ annotationSpaceFillerHolder=null;
+ }
+ public AlignmentPanel(AlignFrame af, final AlignViewport av)
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ alignFrame = af;
+ this.av = av;
+ 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.showAnnotation);
+
+ 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()
+ {
+ public void componentResized(ComponentEvent evt)
+ {
+ setScrollValues(av.getStartRes(), av.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()
+ {
+ public void propertyChange(java.beans.PropertyChangeEvent evt)
+ {
+ if (evt.getPropertyName().equals("alignment"))
+ {
+ PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
+ alignmentChanged();
+ }
+ }
+ });
+
+ }
+
+ public SequenceRenderer getSequenceRenderer()
+ {
+ return seqPanel.seqCanvas.sr;
+ }
+
+ public FeatureRenderer getFeatureRenderer()
+ {
+ return seqPanel.seqCanvas.fr;
+ }
+
+ 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.charHeight + fm.getDescent()));
+ idwidthAdjuster.setSize(new Dimension(10, av.charHeight
+ + 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();
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.updateOverviewImage();
+ }
+ }
+
+ 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(SearchResults 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(SearchResults 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(SearchResults results,
+ boolean redrawOverview)
+ {
+
+ // do we need to scroll the panel?
+ if (results != null && results.getSize() > 0)
+ {
+ int seqIndex = av.alignment.findIndex(results);
+ if (seqIndex == -1)
+ {
+ return false;
+ }
+ SequenceI seq = av.alignment.getSequenceAt(seqIndex);
+ int[] r = results.getResults(seq, 0,av.alignment.getWidth());
+ if (r == null)
+ {
+ if (av.applet.debug) {// DEBUG
+ System.out.println("DEBUG: scroll didn't happen - results not within alignment : "+seq.getStart()+","+seq.getEnd());
+ }
+ return false;
+ }
+ if (av.applet.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];
+ if (start < 0)
+ {
+ return false;
+ }
+ if (end == seq.getEnd())
+ {
+ return false;
+ }
+ 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)
+ {
+ start = av.getColumnSelection().findColumnPosition(ostart);
+ end = av.getColumnSelection().findColumnPosition(end);
+ if (start == end)
+ {
+ if (!scrollToNearest && !av.colSel.isVisible(ostart))
+ {
+ // don't scroll - position isn't visible
+ return false;
+ }
+ }
+ }
+ else
+ {
+ start = ostart;
+ }
+ if (!av.wrapAlignment)
+ {
+ /*
+ 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);
+ }
+
+ /* */
+ if ((av.getStartRes() > end)
+ || (av.getEndRes() < start)
+ || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+ {
+ if (start > av.alignment.getWidth() - hextent)
+ {
+ start = av.alignment.getWidth() - hextent;
+ if (start < 0)
+ {
+ start = 0;
+ }
+
+ }
+ if (seqIndex > av.alignment.getHeight() - vextent)
+ {
+ seqIndex = av.alignment.getHeight() - vextent;
+ if (seqIndex < 0)
+ {
+ seqIndex = 0;
+ }
+ }
+ // System.out.println("trying to scroll to: "+start+" "+seqIndex);
+ setScrollValues(start, seqIndex);
+ }/**/
+ }
+ else
+ {
+ scrollToWrappedVisible(start);
+ }
+ if (redrawOverview && overviewPanel != null)
+ {
+ overviewPanel.setBoxPosition();
+ }
+ paintAlignment(redrawOverview);
+ return true;
+ }
+
+ void scrollToWrappedVisible(int res)
+ {
+ int cwidth = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
+ if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
+ {
+ vscroll.setValue(res / cwidth);
+ av.startRes = vscroll.getValue() * cwidth;
+ }
+ }
+
+ public OverviewPanel getOverviewPanel()
+ {
+ return overviewPanel;
+ }
+
+ public void setOverviewPanel(OverviewPanel op)
+ {
+ overviewPanel = op;
+ }
+
+ public void setAnnotationVisible(boolean b)
+ {
+ if (!av.wrapAlignment)
+ {
+ annotationSpaceFillerHolder.setVisible(b);
+ annotationPanelHolder.setVisible(b);
+ }
+ validate();
+ repaint();
+ }
+
+ /**
+ * automatically adjust annotation panel height for new annotation whilst
+ * ensuring the alignment is still visible.
+ */
+ 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("NEEDS FIXING");
+ }
+ fontChanged();
+ validateAnnotationDimensions(true);
+ apvscroll.addNotify();
+ hscroll.addNotify();
+ validate();
+ paintAlignment(true);
+ }
+ /**
+ * calculate the annotation dimensions and refresh slider values accordingly.
+ * need to do repaints/notifys afterwards.
+ */
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
+ boolean modified=false;
+ int height = annotationPanel.calcPanelHeight();
+ int minsize=0;
+ if (hscroll.isVisible())
+ {
+ height += (minsize=hscroll.getPreferredSize().height);
+ }
+ if (apvscroll.isVisible()) {
+ minsize+=apvscroll.getPreferredSize().height;
+ }
+ int mheight = height;
+ Dimension d=sequenceHolderPanel.getSize(),e=idPanel.getSize();
+ int seqandannot=d.height-scalePanelHolder.getSize().height;
+ // sets initial preferred height
+ if ((height+40) > seqandannot / 2)
+ {
+ height = seqandannot / 2;
+ }
+ if (!adjustPanelHeight)
+ {
+ // maintain same window layout whilst updating sliders
+ height=annotationPanelHolder.getSize().height;
+ }
+
+ if (seqandannot-height<5)
+ {
+ height = seqandannot;
+ }
+ annotationPanel.setSize(new Dimension(d.width,height));
+ alabels.setSize(new Dimension(e.width,height));
+ annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
+ annotationPanelHolder.setSize(new Dimension(d.width, height));
+ seqPanelHolder.setSize(d.width,seqandannot-height);
+ seqPanel.seqCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
+ int s=apvscroll.getValue();
+ if (s>mheight-height)
+ {
+ s = 0;
+ }
+ apvscroll.setValues(s, height, 0, mheight);
+ annotationPanel.setScrollOffset(apvscroll.getValue());
+ alabels.setScrollOffset(apvscroll.getValue());
+ }
+
+ public void setWrapAlignment(boolean wrap)
+ {
+ av.startSeq = 0;
+ av.startRes = 0;
+ scalePanelHolder.setVisible(!wrap);
+
+ hscroll.setVisible(!wrap);
+ idwidthAdjuster.setVisible(!wrap);
+
+ if (wrap)
+ {
+ annotationPanelHolder.setVisible(false);
+ annotationSpaceFillerHolder.setVisible(false);
+ }
+ else if (av.showAnnotation)
+ {
+ annotationPanelHolder.setVisible(true);
+ annotationSpaceFillerHolder.setVisible(true);
+ }
+
+ idSpaceFillerPanel1.setVisible(!wrap);
+
+ fontChanged(); // This is so that the scalePanel is resized correctly
+
+ validate();
+ repaint();
+
+ }
+
+ int hextent = 0;
+
+ int vextent = 0;
+
+ // return value is true if the scroll is valid
+ public boolean scrollUp(boolean up)
+ {
+ if (up)
+ {
+ if (vscroll.getValue() < 1)
+ {
+ return false;
+ }
+ setScrollValues(hscroll.getValue(), vscroll.getValue() - 1);
+ }
+ else
+ {
+ if (vextent + vscroll.getValue() >= av.getAlignment().getHeight())
+ {
+ return false;
+ }
+ setScrollValues(hscroll.getValue(), vscroll.getValue() + 1);
+ }
+
+ repaint();
+ return true;
+ }
+
+ public boolean scrollRight(boolean right)
+ {
+ if (!right)
+ {
+ if (hscroll.getValue() < 1)
+ {
+ return false;
+ }
+ setScrollValues(hscroll.getValue() - 1, vscroll.getValue());
+ }
+ else
+ {
+ if (hextent + hscroll.getValue() >= av.getAlignment().getWidth())
+ {
+ return false;
+ }
+ setScrollValues(hscroll.getValue() + 1, vscroll.getValue());
+ }
+
+ repaint();
+ return true;
+ }
+
+ public void setScrollValues(int x, int y)
+ {
+ int width = av.alignment.getWidth();
+ int height = av.alignment.getHeight();
+
+ if (av.hasHiddenColumns)
+ {
+ width = av.getColumnSelection().findColumnPosition(width);
+ }
+ if (x<0) { x = 0; };
+
+ hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
+ vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
+
+ 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;
+ }
+
+ av.setStartSeq(y);
+
+ int endSeq = y + vextent;
+ if (endSeq > av.alignment.getHeight())
+ {
+ endSeq = av.alignment.getHeight();
+ }
+
+ av.setEndSeq(endSeq);
+ av.setStartRes(x);
+ av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
+
+ hscroll.setValues(x, hextent, 0, width);
+ vscroll.setValues(y, vextent, 0, height);
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.setBoxPosition();
+ }
+ sendViewPosition();
+
+
+ }
+
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ int oldX = av.getStartRes();
+ int oldY = av.getStartSeq();
+
+ if (evt == null || evt.getSource() == apvscroll)
+ {
+ annotationPanel.setScrollOffset(apvscroll.getValue());
+ alabels.setScrollOffset(apvscroll.getValue());
+ // annotationPanel.image=null;
+ // alabels.image=null;
+ // alabels.repaint();
+ // annotationPanel.repaint();
+ }
+ if (evt == null || evt.getSource() == hscroll)
+ {
+ int x = hscroll.getValue();
+ av.setStartRes(x);
+ av.setEndRes(x + seqPanel.seqCanvas.getSize().width
+ / av.getCharWidth() - 1);
+ }
+
+ if (evt == null || evt.getSource() == vscroll)
+ {
+ int offy = vscroll.getValue();
+ if (av.getWrapAlignment())
+ {
+ int rowSize = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
+ av.setStartRes(vscroll.getValue() * rowSize);
+ av.setEndRes((vscroll.getValue() + 1) * rowSize);
+ }
+ else
+ {
+ av.setStartSeq(offy);
+ av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
+ / av.getCharHeight());
+ }
+ }
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.setBoxPosition();
+ }
+
+ int scrollX = av.startRes - oldX;
+ int scrollY = av.startSeq - oldY;
+
+ if (av.getWrapAlignment() || !fastPaint || av.MAC)
+ {
+ repaint();
+ }
+ else
+ {
+ // Make sure we're not trying to draw a panel
+ // larger than the visible window
+ if (scrollX > av.endRes - av.startRes)
+ {
+ scrollX = av.endRes - av.startRes;
+ }
+ else if (scrollX < av.startRes - av.endRes)
+ {
+ scrollX = av.startRes - av.endRes;
+ }
+
+ idPanel.idCanvas.fastPaint(scrollY);
+ seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
+
+ scalePanel.repaint();
+ if (av.getShowAnnotation())
+ {
+ annotationPanel.fastPaint(av.getStartRes() - oldX);
+ }
+ }
+ sendViewPosition();
+
+ }
+ private void sendViewPosition()
+ {
+ StructureSelectionManager.getStructureSelectionManager(av.applet).sendViewPosition(this, av.startRes, av.endRes, av.startSeq, av.endSeq);
+ }
+
+ public void paintAlignment(boolean updateOverview)
+ {
+ repaint();
+
+ if (updateOverview)
+ {
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager(av.applet).sequenceColoursChanged(this);
+
+ if (overviewPanel != null)
+ {
+ overviewPanel.updateOverviewImage();
+ }
+ }
+ }
+
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
+
+ public void paint(Graphics g)
+ {
+ invalidate();
+ Dimension d = idPanel.idCanvas.getSize();
+ idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
+
+ if (av.getWrapAlignment())
+ {
+ int maxwidth = av.alignment.getWidth();
+
+ if (av.hasHiddenColumns)
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ }
+
+ int canvasWidth = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
+
+ if (canvasWidth > 0)
+ {
+ int max = maxwidth / canvasWidth;
+ vscroll.setMaximum(1 + max);
+ vscroll.setUnitIncrement(1);
+ vscroll.setVisibleAmount(1);
+ }
+ }
+ else
+ {
+ setScrollValues(av.getStartRes(), av.getStartSeq());
+ }
+
+ alabels.repaint();
+
+ seqPanel.seqCanvas.repaint();
+ scalePanel.repaint();
+ annotationPanel.repaint();
+ idPanel.idCanvas.repaint();
+ }
+
+ protected Panel sequenceHolderPanel = new Panel();
+
+ protected Scrollbar vscroll = new Scrollbar();
+
+ protected Scrollbar hscroll = new Scrollbar();
+
+ protected Panel seqPanelHolder = new Panel();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ BorderLayout borderLayout3 = new BorderLayout();
+
+ protected Panel scalePanelHolder = new Panel();
+
+ protected Panel idPanelHolder = new Panel();
+
+ BorderLayout borderLayout5 = new BorderLayout();
+
+ protected Panel idSpaceFillerPanel1 = new Panel();
+
+ public Panel annotationSpaceFillerHolder = new Panel();
+
+ BorderLayout borderLayout6 = new BorderLayout();
+
+ BorderLayout borderLayout7 = new BorderLayout();
+
+ Panel hscrollHolder = new Panel();
+
+ BorderLayout borderLayout10 = new BorderLayout();
+
+ protected Panel hscrollFillerPanel = new Panel();
+
+ BorderLayout borderLayout11 = new BorderLayout();
+
+ BorderLayout borderLayout4 = new BorderLayout();
+
+ BorderLayout borderLayout2 = new BorderLayout();
+
+ Panel annotationPanelHolder = new Panel();
+
+ protected Scrollbar apvscroll = new Scrollbar();
+
+ BorderLayout borderLayout12 = new BorderLayout();
+
+ private void jbInit() throws Exception
+ {
+ // idPanelHolder.setPreferredSize(new Dimension(70, 10));
+ this.setLayout(borderLayout7);
+
+ //sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
+ sequenceHolderPanel.setLayout(borderLayout3);
+ seqPanelHolder.setLayout(borderLayout1);
+ scalePanelHolder.setBackground(Color.white);
+
+ // scalePanelHolder.setPreferredSize(new Dimension(10, 30));
+ scalePanelHolder.setLayout(borderLayout6);
+ idPanelHolder.setLayout(borderLayout5);
+ idSpaceFillerPanel1.setBackground(Color.white);
+
+ // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
+ idSpaceFillerPanel1.setLayout(borderLayout11);
+ annotationSpaceFillerHolder.setBackground(Color.white);
+
+ // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
+ annotationSpaceFillerHolder.setLayout(borderLayout4);
+ hscroll.setOrientation(Scrollbar.HORIZONTAL);
+ hscrollHolder.setLayout(borderLayout10);
+ hscrollFillerPanel.setBackground(Color.white);
+ apvscroll.setOrientation(Scrollbar.VERTICAL);
+ apvscroll.setVisible(true);
+ apvscroll.addAdjustmentListener(this);
+
+ annotationPanelHolder.setBackground(Color.white);
+ annotationPanelHolder.setLayout(borderLayout12);
+ 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)
+ {
+ // TODO: this should be merged with other annotation update stuff - that
+ // sits on AlignViewport
+ boolean updateCalcs = false;
+ boolean conv = av.isShowGroupConservation();
+ boolean cons = av.isShowGroupConsensus();
+ boolean showprf = av.isShowSequenceLogo();
+ boolean showConsHist = av.isShowConsensusHistogram();
+
+ boolean sortg = true;
+
+ // remove old automatic annotation
+ // add any new annotation
+
+ Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
+ // intersect alignment annotation with alignment groups
+
+ AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
+ Hashtable oldrfs = new Hashtable();
+ if (aan != null)
+ {
+ for (int an = 0; an < aan.length; an++)
+ {
+ if (aan[an].autoCalculated && aan[an].groupRef != null)
+ {
+ oldrfs.put(aan[an].groupRef, aan[an].groupRef);
+ av.alignment.deleteAnnotation(aan[an]);
+ aan[an] = null;
+ }
+ }
+ }
+ SequenceGroup sg;
+ if (gr != null)
+ {
+ for (int g = 0; g < gr.size(); g++)
+ {
+ updateCalcs = false;
+ sg = (SequenceGroup) gr.elementAt(g);
+ if (applyGlobalSettings || !oldrfs.containsKey(sg))
+ {
+ // set defaults for this group's conservation/consensus
+ sg.setshowSequenceLogo(showprf);
+ sg.setShowConsensusHistogram(showConsHist);
+ }
+ if (conv)
+ {
+ updateCalcs = true;
+ av.alignment.addAnnotation(sg.getConservationRow(), 0);
+ }
+ if (cons)
+ {
+ updateCalcs = true;
+ av.alignment.addAnnotation(sg.getConsensus(), 0);
+ }
+ // refresh the annotation rows
+ if (updateCalcs)
+ {
+ sg.recalcConservation();
+ }
+ }
+ }
+ oldrfs.clear();
+ adjustAnnotationHeight();
+ }
+
+ @Override
+ public AlignmentI getAlignment()
+ {
+ return av.alignment;
+ }
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager.getStructureSelectionManager(av.applet);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff