-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import javax.swing.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import java.util.*;\r
-import java.awt.image.*;\r
-\r
-public class AnnotationPanel extends JPanel implements MouseListener, MouseMotionListener, ActionListener, AdjustmentListener\r
-{\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- int activeRow =-1;\r
-\r
- ArrayList activeRes;\r
- static String HELIX ="Helix";\r
- static String SHEET ="Sheet";\r
- static String LABEL ="Label";\r
- static String REMOVE="Remove Annotation";\r
- static String COLOUR="Colour";\r
- static Color HELIX_COLOUR = Color.red.darker();\r
- static Color SHEET_COLOUR = Color.green.darker().darker();\r
-\r
-\r
- BufferedImage image;\r
- Graphics2D gg;\r
- FontMetrics fm;\r
- int imgWidth=0;\r
-\r
- boolean fastPaint = false;\r
-\r
- public static int GRAPH_HEIGHT = 40;\r
-\r
-\r
-\r
- public AnnotationPanel(AlignmentPanel ap)\r
- {\r
- this.ap = ap;\r
- av = ap.av;\r
- this.setLayout(null);\r
- addMouseListener(this);\r
- addMouseMotionListener(this);\r
- adjustPanelHeight();\r
-\r
-\r
- ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener( this );\r
- }\r
-\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
- {\r
- ap.alabels.setScrollOffset( -evt.getValue() );\r
- }\r
-\r
- public void adjustPanelHeight()\r
- {\r
- // setHeight of panels\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
- int height = 0;\r
- if(aa!=null)\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if(!aa[i].visible)\r
- continue;\r
-\r
- aa[i].height = 0;\r
-\r
- if(aa[i].hasText)\r
- aa[i].height += av.charHeight;\r
- if (aa[i].hasIcons)\r
- aa[i].height += 16;\r
-\r
- if (aa[i].isGraph)\r
- aa[i].height += GRAPH_HEIGHT;\r
-\r
- if(aa[i].height==0)\r
- aa[i].height = 20;\r
- height += aa[i].height;\r
- }\r
- else height=20;\r
- this.setPreferredSize(new Dimension(1, height));\r
-\r
- }\r
-\r
- public void addEditableColumn(int i)\r
- {\r
- if(activeRow==-1)\r
- {\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- for(int j=0; j<aa.length; j++)\r
- if(aa[j].editable)\r
- {\r
- activeRow = j;\r
- break;\r
- }\r
- }\r
-\r
- if(activeRes==null)\r
- {\r
- activeRes = new ArrayList();\r
- activeRes.add(String.valueOf(i));\r
- return;\r
- }\r
-\r
- activeRes.add(String.valueOf(i));\r
-\r
- }\r
-\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
-\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- Annotation [] anot = aa[activeRow].annotations;\r
-\r
- if(evt.getActionCommand().equals(REMOVE))\r
- {\r
- for(int i=0; i<activeRes.size(); i++)\r
- {\r
- anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
- anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
- }\r
- }\r
- else if(evt.getActionCommand().equals(LABEL))\r
- {\r
- String label = JOptionPane.showInputDialog(this, "Enter Label ", "Enter label", JOptionPane.QUESTION_MESSAGE );\r
- if(label==null)\r
- label = "";\r
-\r
- if(label.length()>0 && !aa[activeRow].hasText)\r
- aa[activeRow].hasText = true;\r
-\r
- for(int i=0; i<activeRes.size(); i++)\r
- {\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
- if(anot[index]==null)\r
- anot[index] = new Annotation(label, "", ' ',0);\r
- anot[index].displayCharacter = label;\r
- }\r
- }\r
- else if(evt.getActionCommand().equals(COLOUR))\r
- {\r
- Color col = JColorChooser.showDialog(this, "Choose foreground colour", Color.black);\r
- for (int i = 0; i < activeRes.size(); i++)\r
- {\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
- if (anot[index] == null)\r
- anot[index] = new Annotation("", "", ' ', 0);\r
- anot[index].colour = col;\r
- }\r
- }\r
- else // HELIX OR SHEET\r
- {\r
- char type = 0;\r
- String symbol = "\u03B1";\r
- if(evt.getActionCommand().equals(HELIX))\r
- type = 'H';\r
- else if(evt.getActionCommand().equals(SHEET))\r
- {\r
- type = 'E';\r
- symbol = "\u03B2";\r
- }\r
-\r
- if(!aa[activeRow].hasIcons)\r
- aa[activeRow].hasIcons = true;\r
-\r
-\r
- String label = JOptionPane.showInputDialog("Enter a label for the structure?", symbol );\r
- if(label==null)\r
- label="";\r
-\r
- if(label.length()>0 && !aa[activeRow].hasText)\r
- aa[activeRow].hasText = true;\r
-\r
- for(int i=0; i<activeRes.size(); i++)\r
- {\r
- int index = Integer.parseInt(activeRes.get(i).toString());\r
- if (anot[index] == null)\r
- {\r
- anot[index] = new Annotation(label, "", type, 0);\r
- }\r
-\r
- anot[ index ].secondaryStructure = type;\r
- anot[ index ].displayCharacter = label;\r
- }\r
- }\r
-\r
- adjustPanelHeight();\r
- activeRes = null;\r
- repaint();\r
- return;\r
-\r
-\r
- }\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- if (SwingUtilities.isRightMouseButton(evt))\r
- {\r
- if(activeRes==null)\r
- return;\r
-\r
- JPopupMenu pop = new JPopupMenu("Structure type");\r
- JMenuItem item = new JMenuItem(HELIX);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(SHEET);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(LABEL);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(COLOUR);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- item = new JMenuItem(REMOVE);\r
- item.addActionListener(this);\r
- pop.add(item);\r
- pop.show(this, evt.getX(), evt.getY());\r
- return;\r
- }\r
-\r
-\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- if(aa==null)\r
- return;\r
-\r
- int height = 0;\r
- activeRow = -1;\r
- for(int i=0; i<aa.length; i++)\r
- {\r
- height+= aa[i].height;\r
-\r
- if(evt.getY()<height)\r
- {\r
- if(!aa[i].editable)\r
- {\r
- activeRes = null;\r
- continue;\r
- }\r
-\r
- activeRow = i;\r
- break;\r
- }\r
- }\r
-\r
-\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
-\r
- if(evt.isControlDown() || evt.isAltDown())\r
- addEditableColumn(res);\r
-\r
- else if(evt.isShiftDown())\r
- {\r
-\r
- if(activeRes==null)\r
- activeRes=new ArrayList();\r
- else\r
- {\r
- int start = Integer.parseInt( activeRes.get( activeRes.size()-1 ).toString() );\r
- int end = res;\r
- if(end<start)\r
- {\r
- int temp = end;\r
- end = start;\r
- start = temp;\r
- }\r
- for(int n=start; n<=end; n++)\r
- addEditableColumn(n);\r
-\r
- }\r
- }\r
- else\r
- {\r
- activeRes = new ArrayList();\r
- activeRes.add( String.valueOf(res) );\r
- }\r
-\r
- repaint();\r
-\r
- }\r
- public void mouseReleased(MouseEvent evt)\r
- { }\r
- public void mouseEntered(MouseEvent evt)\r
- { }\r
- public void mouseExited(MouseEvent evt)\r
- { }\r
- public void mouseDragged(MouseEvent evt)\r
- { }\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- ToolTipManager.sharedInstance().registerComponent(this);\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
- if(aa==null)\r
- return;\r
-\r
- int row = -1;\r
- int height=0;\r
- for(int i=0; i<aa.length; i++)\r
- {\r
-\r
- if( aa[i].visible )\r
- height += aa[i].height;\r
-\r
- if(evt.getY()<height)\r
- {\r
- row = i;\r
- break;\r
- }\r
- }\r
-\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
- if(row>-1 && res<aa[row].annotations.length && aa[row].annotations[res]!=null)\r
- {\r
- this.setToolTipText(aa[row].annotations[res].description);\r
- StringBuffer text = new StringBuffer("Sequence position " + (res + 1) +\r
- " " +\r
- aa[row].annotations[res].description);\r
- ap.alignFrame.statusBar.setText(text.toString());\r
- }\r
-\r
-\r
- }\r
- public void mouseClicked(MouseEvent evt) {}\r
-\r
-\r
- public void paintComponent(Graphics g)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0,0,getWidth(), getHeight());\r
-\r
- if(fastPaint)\r
- {\r
- g.drawImage(image, 0, 0, this);\r
- fastPaint = false;\r
- return;\r
- }\r
-\r
- imgWidth = (av.endRes-av.startRes+1) *av.charWidth;\r
-\r
- image = new BufferedImage(imgWidth,\r
- ap.annotationPanel.getHeight(),\r
- BufferedImage.TYPE_INT_RGB);\r
- gg = (Graphics2D) image.getGraphics();\r
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
- fm = gg.getFontMetrics();\r
- gg.setFont(av.getFont());\r
-\r
- drawComponent( gg, av.startRes, av.endRes+1);\r
- g.drawImage( image, 0, 0, this);\r
-\r
- }\r
-\r
- public void fastPaint(int horizontal)\r
-{\r
- if( horizontal == 0\r
- || av.alignment.getAlignmentAnnotation()==null\r
- || av.alignment.getAlignmentAnnotation().length<1\r
- )\r
- {\r
- repaint();\r
- return;\r
- }\r
-\r
- gg.copyArea( 0,0, imgWidth, getHeight(), -horizontal*av.charWidth, 0 );\r
- int sr=av.startRes, er=av.endRes+1, transX=0;\r
-\r
- if(horizontal>0) // scrollbar pulled right, image to the left\r
- {\r
- transX = (er-sr-horizontal)*av.charWidth;\r
- sr = er - horizontal ;\r
- }\r
- else if(horizontal<0)\r
- {\r
- er = sr-horizontal;\r
- }\r
-\r
-\r
- gg.translate(transX, 0);\r
-\r
- drawComponent(gg, sr, er);\r
-\r
- gg.translate( -transX, 0 );\r
-\r
- fastPaint = true;\r
- repaint();\r
-}\r
-\r
-\r
- public void drawComponent(Graphics2D g, int startRes, int endRes)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0,0,(endRes-startRes) *av.charWidth, getHeight());\r
- if(av.alignment.getAlignmentAnnotation()==null || av.alignment.getAlignmentAnnotation().length<1)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0,0,getWidth(), getHeight());\r
- g.setColor(Color.black);\r
- g.drawString("Alignment has no annotations",20,15);\r
- return;\r
- }\r
-\r
- AlignmentAnnotation [] aa = av.alignment.getAlignmentAnnotation();\r
-\r
- int j, x=0, y=0;\r
- char [] lastSS = new char[aa.length];\r
- int [] lastSSX= new int[aa.length] ;\r
- int iconOffset = av.charHeight/2;\r
- boolean validRes = false;\r
- //\u03B2 \u03B1\r
-\r
- for(int i=0; i<aa.length; i++)\r
- {\r
- AlignmentAnnotation row = aa[i];\r
- if(!row.visible)\r
- continue;\r
-\r
- if(row.isGraph)\r
- {\r
- // this is so that we draw the characters below the graph\r
- y += row.height;\r
- if(row.hasText)\r
- y -= av.charHeight;\r
- }\r
- if(row.hasText)\r
- iconOffset = av.charHeight/2;\r
- else\r
- iconOffset = 0;\r
-\r
- for(j=startRes; j<endRes; j++)\r
- {\r
- validRes = row.annotations[j]==null?false:true;\r
-\r
- x = (j-startRes)*av.charWidth;\r
-\r
-\r
- if(activeRow==i)\r
- {\r
-\r
- g.setColor(Color.red);\r
-\r
- if(activeRes!=null)\r
- for (int n = 0; n < activeRes.size(); n++)\r
- {\r
- int v = Integer.parseInt(activeRes.get(n).toString()) ;\r
- if (v == j)\r
- g.fillRect( (j-startRes) * av.charWidth, y, av.charWidth, row.height);\r
- }\r
- }\r
-\r
-\r
-\r
- if(validRes && row.annotations[j].displayCharacter.length()>0)\r
- {\r
- int charOffset = (av.charWidth -\r
- fm.charWidth(row.annotations[j].displayCharacter.\r
- charAt(0))) / 2;\r
- g.setColor( row.annotations[j].colour);\r
- if(j==0)\r
- {\r
- if (row.annotations[0].secondaryStructure == 'H'\r
- || row.annotations[0].secondaryStructure == 'E')\r
- g.drawString(row.annotations[j].displayCharacter, x,\r
- y + iconOffset + 2);\r
- }\r
- else if( (row.annotations[j].secondaryStructure=='H'\r
- || row.annotations[j].secondaryStructure=='E') &&\r
- (row.annotations[j-1]==null ||\r
- row.annotations[j].secondaryStructure!=row.annotations[j-1].secondaryStructure))\r
-\r
- g.drawString(row.annotations[j].displayCharacter, x, y + iconOffset + 2);\r
-\r
- if(!row.hasIcons)\r
- g.drawString(row.annotations[j].displayCharacter, x + charOffset,\r
- y + iconOffset + 2);\r
- }\r
-\r
- if(row.hasIcons)\r
- if(!validRes || row.annotations[j].secondaryStructure!=lastSS[i])\r
- {\r
- switch (lastSS[i])\r
- {\r
- case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y+4 + iconOffset, x-lastSSX[i], 7, 8, 8);\r
- break;\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset, x-lastSSX[i]-4, 7);\r
- g.fillPolygon(new int[] {x - 4, x- 4, x }\r
- , new int[]{y+ iconOffset, y + 14+ iconOffset, y + 8+ iconOffset}, 3);\r
- break;\r
- case 'C':\r
- break;\r
- default :\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
- break;\r
- }\r
-\r
- if(validRes)\r
- lastSS[i] = row.annotations[j].secondaryStructure;\r
- else\r
- lastSS[i] = ' ';\r
- lastSSX[i] = x;\r
- }\r
-\r
- if (validRes && row.isGraph)\r
- {\r
- g.setColor(new Color(0,0,180));\r
- int height = (int)((row.annotations[j].value / row.graphMax)*GRAPH_HEIGHT);\r
-\r
- if(row.windowLength>1)\r
- {\r
- int total =0;\r
- for(int i2=j- (row.windowLength/2); i2<j+(row.windowLength/2); i2++)\r
- {\r
- if(i2<0 || i2>=av.alignment.getWidth())\r
- continue;\r
-\r
- total += row.annotations[i2].value;\r
- }\r
-\r
- total/=row.windowLength;\r
- height = (int)( (total / row.graphMax) *GRAPH_HEIGHT);\r
-\r
- }\r
- g.setColor(row.annotations[j].colour);\r
- g.fillRect(x, y-height, av.charWidth, height );\r
- }\r
-\r
-\r
- }\r
-\r
- x+=av.charWidth;\r
-\r
- if(row.hasIcons)\r
- switch (lastSS[i])\r
- {\r
- case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y+4+ iconOffset, x - lastSSX[i], 7, 8, 8);\r
- break;\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
- g.fillRect(lastSSX[i], y + 4+ iconOffset, x - lastSSX[i] - 4, 7);\r
- g.fillPolygon(new int[]\r
- {x - 4, x - 4, x}\r
- , new int[]\r
- {y + iconOffset, y + 14+ iconOffset, y + 7+ iconOffset}\r
- , 3);\r
- break;\r
- case 'C':\r
- break;\r
- default:\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y+6+ iconOffset, x-lastSSX[i], 2);\r
- break;\r
-\r
- }\r
-\r
- if(row.isGraph && row.hasText)\r
- y+=av.charHeight;\r
- if(!row.isGraph)\r
- y+=aa[i].height;\r
- }\r
- }\r
-\r
- // used by overview window\r
- public void drawGraph(Graphics g, AlignmentAnnotation aa,int width, int y)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0,0,width, y);\r
- g.setColor(new Color(0,0,180));\r
- int x = 0;\r
- for(int j=0; j<aa.annotations.length; j++)\r
- {\r
- g.setColor(new Color(0, 0, 180));\r
- int height = (int) ( (aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT );\r
- g.fillRect(x, y - height, av.charWidth, height);\r
- x+=av.charWidth;\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.gui;
+
+import java.awt.AlphaComposite;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.Rectangle;
+import java.awt.RenderingHints;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.JMenuItem;
+import javax.swing.JPanel;
+import javax.swing.JPopupMenu;
+import javax.swing.Scrollable;
+import javax.swing.ToolTipManager;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactMatrixI;
+import jalview.datamodel.ContactRange;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.AwtRenderPanelI;
+import jalview.renderer.ContactGeometry;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
+
+/**
+ * AnnotationPanel displays visible portion of annotation rows below unwrapped
+ * alignment
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
+ MouseListener, MouseWheelListener, MouseMotionListener,
+ ActionListener, AdjustmentListener, Scrollable, ViewportListenerI
+{
+ enum DragMode
+ {
+ Select, Resize, Undefined, MatrixSelect
+ };
+
+ String HELIX = MessageManager.getString("label.helix");
+
+ String SHEET = MessageManager.getString("label.sheet");
+
+ /**
+ * For RNA secondary structure "stems" aka helices
+ */
+ String STEM = MessageManager.getString("label.rna_helix");
+
+ String LABEL = MessageManager.getString("label.label");
+
+ String REMOVE = MessageManager.getString("label.remove_annotation");
+
+ String COLOUR = MessageManager.getString("action.colour");
+
+ public final Color HELIX_COLOUR = Color.red.darker();
+
+ public final Color SHEET_COLOUR = Color.green.darker().darker();
+
+ public final Color STEM_COLOUR = Color.blue.darker();
+
+ /** DOCUMENT ME!! */
+ public AlignViewport av;
+
+ AlignmentPanel ap;
+
+ public int activeRow = -1;
+
+ public BufferedImage image;
+
+ public volatile BufferedImage fadedImage;
+
+ // private Graphics2D gg;
+
+ public FontMetrics fm;
+
+ public int imgWidth = 0;
+
+ boolean fastPaint = false;
+
+ // Used For mouse Dragging and resizing graphs
+ int graphStretch = -1;
+
+ int mouseDragLastX = -1;
+
+ int mouseDragLastY = -1;
+
+ int firstDragX = -1;
+
+ int firstDragY = -1;
+
+ DragMode dragMode = DragMode.Undefined;
+
+ boolean mouseDragging = false;
+
+ // for editing cursor
+ int cursorX = 0;
+
+ int cursorY = 0;
+
+ public final AnnotationRenderer renderer;
+
+ private MouseWheelListener[] _mwl;
+
+ private boolean notJustOne;
+
+ /**
+ * Creates a new AnnotationPanel object.
+ *
+ * @param ap
+ * DOCUMENT ME!
+ */
+ public AnnotationPanel(AlignmentPanel ap)
+ {
+ ToolTipManager.sharedInstance().registerComponent(this);
+ ToolTipManager.sharedInstance().setInitialDelay(0);
+ ToolTipManager.sharedInstance().setDismissDelay(10000);
+ this.ap = ap;
+ av = ap.av;
+ this.setLayout(null);
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ ap.annotationScroller.getVerticalScrollBar()
+ .addAdjustmentListener(this);
+ // save any wheel listeners on the scroller, so we can propagate scroll
+ // events to them.
+ _mwl = ap.annotationScroller.getMouseWheelListeners();
+ // and then set our own listener to consume all mousewheel events
+ ap.annotationScroller.addMouseWheelListener(this);
+ renderer = new AnnotationRenderer();
+
+ av.getRanges().addPropertyChangeListener(this);
+ }
+
+ public AnnotationPanel(AlignViewport av)
+ {
+ this.av = av;
+ renderer = new AnnotationRenderer();
+ }
+
+ @Override
+ public void mouseWheelMoved(MouseWheelEvent e)
+ {
+ if (e.isShiftDown())
+ {
+ e.consume();
+ double wheelRotation = e.getPreciseWheelRotation();
+ if (wheelRotation > 0)
+ {
+ av.getRanges().scrollRight(true);
+ }
+ else if (wheelRotation < 0)
+ {
+ av.getRanges().scrollRight(false);
+ }
+ }
+ else
+ {
+ // TODO: find the correct way to let the event bubble up to
+ // ap.annotationScroller
+ for (MouseWheelListener mwl : _mwl)
+ {
+ if (mwl != null)
+ {
+ mwl.mouseWheelMoved(e);
+ }
+ if (e.isConsumed())
+ {
+ break;
+ }
+ }
+ }
+ }
+
+ @Override
+ public Dimension getPreferredScrollableViewportSize()
+ {
+ Dimension ps = getPreferredSize();
+ return new Dimension(ps.width, adjustForAlignFrame(false, ps.height));
+ }
+
+ @Override
+ public int getScrollableBlockIncrement(Rectangle visibleRect,
+ int orientation, int direction)
+ {
+ return 30;
+ }
+
+ @Override
+ public boolean getScrollableTracksViewportHeight()
+ {
+ return false;
+ }
+
+ @Override
+ public boolean getScrollableTracksViewportWidth()
+ {
+ return true;
+ }
+
+ @Override
+ public int getScrollableUnitIncrement(Rectangle visibleRect,
+ int orientation, int direction)
+ {
+ return 30;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * java.awt.event.AdjustmentListener#adjustmentValueChanged(java.awt.event
+ * .AdjustmentEvent)
+ */
+ @Override
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ // update annotation label display
+ ap.getAlabels().setScrollOffset(-evt.getValue());
+ }
+
+ /**
+ * Calculates the height of the annotation displayed in the annotation panel.
+ * Callers should normally call the ap.adjustAnnotationHeight method to ensure
+ * all annotation associated components are updated correctly.
+ *
+ */
+ public int adjustPanelHeight()
+ {
+ int height = av.calcPanelHeight();
+ this.setPreferredSize(new Dimension(1, height));
+ if (ap != null)
+ {
+ // revalidate only when the alignment panel is fully constructed
+ ap.validate();
+ }
+
+ return height;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void actionPerformed(ActionEvent evt)
+ {
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ if (aa == null)
+ {
+ return;
+ }
+ Annotation[] anot = aa[activeRow].annotations;
+
+ if (anot.length < av.getColumnSelection().getMax())
+ {
+ Annotation[] temp = new Annotation[av.getColumnSelection().getMax()
+ + 2];
+ System.arraycopy(anot, 0, temp, 0, anot.length);
+ anot = temp;
+ aa[activeRow].annotations = anot;
+ }
+
+ String action = evt.getActionCommand();
+ if (action.equals(REMOVE))
+ {
+ for (int index : av.getColumnSelection().getSelected())
+ {
+ if (av.getAlignment().getHiddenColumns().isVisible(index))
+ {
+ anot[index] = null;
+ }
+ }
+ }
+ else if (action.equals(LABEL))
+ {
+ String exMesg = collectAnnotVals(anot, LABEL);
+ String label = JvOptionPane.showInputDialog(
+ MessageManager.getString("label.enter_label"), exMesg);
+
+ if (label == null)
+ {
+ return;
+ }
+
+ if ((label.length() > 0) && !aa[activeRow].hasText)
+ {
+ aa[activeRow].hasText = true;
+ }
+
+ for (int index : av.getColumnSelection().getSelected())
+ {
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
+ {
+ continue;
+ }
+
+ if (anot[index] == null)
+ {
+ anot[index] = new Annotation(label, "", ' ', 0);
+ }
+ else
+ {
+ anot[index].displayCharacter = label;
+ }
+ }
+ }
+ else if (action.equals(COLOUR))
+ {
+ final Annotation[] fAnot = anot;
+ String title = MessageManager
+ .getString("label.select_foreground_colour");
+ ColourChooserListener listener = new ColourChooserListener()
+ {
+ @Override
+ public void colourSelected(Color c)
+ {
+ HiddenColumns hiddenColumns = av.getAlignment()
+ .getHiddenColumns();
+ for (int index : av.getColumnSelection().getSelected())
+ {
+ if (hiddenColumns.isVisible(index))
+ {
+ if (fAnot[index] == null)
+ {
+ fAnot[index] = new Annotation("", "", ' ', 0);
+ }
+ fAnot[index].colour = c;
+ }
+ }
+ };
+ };
+ JalviewColourChooser.showColourChooser(this, title, Color.black,
+ listener);
+ }
+ else
+ // HELIX, SHEET or STEM
+ {
+ char type = 0;
+ String symbol = "\u03B1"; // alpha
+
+ if (action.equals(HELIX))
+ {
+ type = 'H';
+ }
+ else if (action.equals(SHEET))
+ {
+ type = 'E';
+ symbol = "\u03B2"; // beta
+ }
+
+ // Added by LML to color stems
+ else if (action.equals(STEM))
+ {
+ type = 'S';
+ int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
+ symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
+ }
+
+ if (!aa[activeRow].hasIcons)
+ {
+ aa[activeRow].hasIcons = true;
+ }
+
+ String label = JvOptionPane.showInputDialog(MessageManager
+ .getString("label.enter_label_for_the_structure"), symbol);
+
+ if (label == null)
+ {
+ return;
+ }
+
+ if ((label.length() > 0) && !aa[activeRow].hasText)
+ {
+ aa[activeRow].hasText = true;
+ if (action.equals(STEM))
+ {
+ aa[activeRow].showAllColLabels = true;
+ }
+ }
+ for (int index : av.getColumnSelection().getSelected())
+ {
+ if (!av.getAlignment().getHiddenColumns().isVisible(index))
+ {
+ continue;
+ }
+
+ if (anot[index] == null)
+ {
+ anot[index] = new Annotation(label, "", type, 0);
+ }
+
+ anot[index].secondaryStructure = type != 'S' ? type
+ : label.length() == 0 ? ' ' : label.charAt(0);
+ anot[index].displayCharacter = label;
+
+ }
+ }
+
+ av.getAlignment().validateAnnotation(aa[activeRow]);
+ ap.alignmentChanged();
+ ap.alignFrame.setMenusForViewport();
+ adjustPanelHeight();
+ repaint();
+
+ return;
+ }
+
+ /**
+ * Returns any existing annotation concatenated as a string. For each
+ * annotation, takes the description, if any, else the secondary structure
+ * character (if type is HELIX, SHEET or STEM), else the display character (if
+ * type is LABEL).
+ *
+ * @param anots
+ * @param type
+ * @return
+ */
+ private String collectAnnotVals(Annotation[] anots, String type)
+ {
+ // TODO is this method wanted? why? 'last' is not used
+
+ StringBuilder collatedInput = new StringBuilder(64);
+ String last = "";
+ ColumnSelection viscols = av.getColumnSelection();
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+
+ /*
+ * the selection list (read-only view) is in selection order, not
+ * column order; make a copy so we can sort it
+ */
+ List<Integer> selected = new ArrayList<>(viscols.getSelected());
+ Collections.sort(selected);
+ for (int index : selected)
+ {
+ // always check for current display state - just in case
+ if (!hidden.isVisible(index))
+ {
+ continue;
+ }
+ String tlabel = null;
+ if (anots[index] != null)
+ { // LML added stem code
+ if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM)
+ || type.equals(LABEL))
+ {
+ tlabel = anots[index].description;
+ if (tlabel == null || tlabel.length() < 1)
+ {
+ if (type.equals(HELIX) || type.equals(SHEET)
+ || type.equals(STEM))
+ {
+ tlabel = "" + anots[index].secondaryStructure;
+ }
+ else
+ {
+ tlabel = "" + anots[index].displayCharacter;
+ }
+ }
+ }
+ if (tlabel != null && !tlabel.equals(last))
+ {
+ if (last.length() > 0)
+ {
+ collatedInput.append(" ");
+ }
+ collatedInput.append(tlabel);
+ }
+ }
+ }
+ return collatedInput.toString();
+ }
+
+ /**
+ * Action on right mouse pressed on Mac is to show a pop-up menu for the
+ * annotation. Action on left mouse pressed is to find which annotation is
+ * pressed and mark the start of a column selection or graph resize operation.
+ *
+ * @param evt
+ */
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ if (aa == null)
+ {
+ return;
+ }
+ mouseDragLastX = evt.getX();
+ mouseDragLastY = evt.getY();
+
+ /*
+ * add visible annotation heights until we reach the y
+ * position, to find which annotation it is in
+ */
+ int height = 0;
+ activeRow = -1;
+ int yOffset = 0;
+ // todo could reuse getRowIndexAndOffset ?
+ final int y = evt.getY();
+
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].visible)
+ {
+ height += aa[i].height;
+ }
+
+ if (y < height)
+ {
+ if (aa[i].editable)
+ {
+ activeRow = i;
+ }
+ else if (aa[i].graph != 0)
+ {
+ /*
+ * we have clicked on a resizable graph annotation
+ */
+ graphStretch = i;
+ yOffset = height - y;
+ }
+ break;
+ }
+ }
+
+ /*
+ * isPopupTrigger fires in mousePressed on Mac,
+ * not until mouseRelease on Windows
+ */
+ if (evt.isPopupTrigger() && activeRow != -1)
+ {
+ showPopupMenu(y, evt.getX());
+ return;
+ }
+
+ if (graphStretch != -1)
+ {
+
+ if (aa[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP)
+ {
+ // data in row has position on y as well as x axis
+ if (evt.isAltDown() || evt.isAltGraphDown())
+ {
+ dragMode = DragMode.MatrixSelect;
+ firstDragX = mouseDragLastX;
+ firstDragY = mouseDragLastY;
+ }
+ }
+ }
+ else
+ {
+ // no row (or row that can be adjusted) was pressed. Simulate a ruler click
+ ap.getScalePanel().mousePressed(evt);
+ }
+ }
+
+ /**
+ * checks whether the annotation row under the mouse click evt's handles the
+ * event
+ *
+ * @param evt
+ * @return false if evt was not handled
+ */
+ boolean matrix_clicked(MouseEvent evt)
+ {
+ int[] rowIndex = getRowIndexAndOffset(evt.getY(),
+ av.getAlignment().getAlignmentAnnotation());
+ if (rowIndex == null)
+ {
+ jalview.bin.Console
+ .error("IMPLEMENTATION ERROR: matrix click out of range.");
+ return false;
+ }
+ int yOffset = rowIndex[1];
+
+ AlignmentAnnotation clicked = av.getAlignment()
+ .getAlignmentAnnotation()[rowIndex[0]];
+ if (clicked.graph != AlignmentAnnotation.CONTACT_MAP)
+ {
+ return false;
+ }
+
+ // TODO - use existing threshold to select related sections of matrix
+ GraphLine thr = clicked.getThreshold();
+
+ int currentX = getColumnForXPos(evt.getX());
+ ContactListI forCurrentX = av.getContactList(clicked, currentX);
+ if (forCurrentX != null)
+ {
+ ContactGeometry cXcgeom = new ContactGeometry(forCurrentX,
+ clicked.graphHeight);
+ ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset,
+ yOffset);
+ /**
+ * start and end range corresponding to the row range under the mouse at
+ * column currentX
+ */
+ int fr, to;
+ fr = Math.min(cXci.cStart, cXci.cEnd);
+ to = Math.max(cXci.cStart, cXci.cEnd);
+
+ // double click selects the whole group
+ if (evt.getClickCount() == 2)
+ {
+ ContactMatrixI matrix = av.getContactMatrix(clicked);
+
+ if (matrix != null)
+ {
+ // simplest approach is to select all group containing column
+ if (matrix.hasGroups())
+ {
+ SequenceI rseq = clicked.sequenceRef;
+ BitSet grp = matrix.getGroupsFor(currentX);
+ // TODO: cXci needs to be mapped to real groups
+ for (int c = fr; c <= to; c++)
+ {
+ BitSet additionalGrp = matrix.getGroupsFor(c);
+ grp.or(additionalGrp);
+ }
+ HiddenColumns hc = av.getAlignment().getHiddenColumns();
+ for (int p = grp.nextSetBit(0); p >= 0; p = grp
+ .nextSetBit(p + 1))
+ {
+ int offp = (rseq != null)
+ ? rseq.findIndex(rseq.getStart() - 1 + p)
+ : p;
+
+ if (!av.hasHiddenColumns() || hc.isVisible(offp))
+ {
+ av.getColumnSelection().addElement(offp);
+ }
+ }
+ }
+ // possible alternative for interactive selection - threshold
+ // gives 'ceiling' for forming a cluster
+ // when a row+column is selected, farthest common ancestor less
+ // than thr is used to compute cluster
+
+ }
+ }
+ else
+ {
+ // select corresponding range in segment under mouse
+ {
+ int[] rng = forCurrentX.getMappedPositionsFor(fr, to);
+ if (rng != null)
+ {
+ av.getColumnSelection().addRangeOfElements(rng, true);
+ }
+ av.getColumnSelection().addElement(currentX);
+ }
+ // PAE SPECIFIC
+ // and also select everything lower than the max range adjacent
+ // (kind of works)
+ if (evt.isControlDown()
+ && PAEContactMatrix.PAEMATRIX.equals(clicked.getCalcId()))
+ {
+ int c = fr - 1;
+ ContactRange cr = forCurrentX.getRangeFor(fr, to);
+ double cval;
+ // TODO: could use GraphLine instead of arbitrary picking
+ // TODO: could report mean/median/variance for partitions
+ // (contiguous selected vs unselected regions and inter-contig
+ // regions)
+ // controls feathering - what other elements in row/column
+ // should we select
+ double thresh = cr.getMean() + (cr.getMax() - cr.getMean()) * .15;
+ while (c > 0)
+ {
+ cval = forCurrentX.getContactAt(c);
+ if (// cr.getMin() <= cval &&
+ cval <= thresh)
+ {
+ int[] cols = forCurrentX.getMappedPositionsFor(c, c);
+ if (cols != null)
+ {
+ av.getColumnSelection().addRangeOfElements(cols, true);
+ }
+ else
+ {
+ break;
+ }
+ }
+ c--;
+ }
+ c = to;
+ while (c < forCurrentX.getContactHeight())
+ {
+ cval = forCurrentX.getContactAt(c);
+ if (// cr.getMin() <= cval &&
+ cval <= thresh)
+ {
+ int[] cols = forCurrentX.getMappedPositionsFor(c, c);
+ if (cols != null)
+ {
+ av.getColumnSelection().addRangeOfElements(cols, true);
+ }
+ }
+ else
+ {
+ break;
+ }
+ c++;
+
+ }
+ }
+ }
+ }
+ ap.paintAlignment(false, false);
+ PaintRefresher.Refresh(ap, av.getSequenceSetId());
+ av.sendSelection();
+ return true;
+ }
+ /**
+ * Construct and display a context menu at the right-click position
+ *
+ * @param y
+ * @param x
+ */
+ void showPopupMenu(final int y, int x)
+ {
+ if (av.getColumnSelection() == null
+ || av.getColumnSelection().isEmpty())
+ {
+ return;
+ }
+
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.structure_type"));
+ JMenuItem item;
+ /*
+ * Just display the needed structure options
+ */
+ if (av.getAlignment().isNucleotide())
+ {
+ item = new JMenuItem(STEM);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ else
+ {
+ item = new JMenuItem(HELIX);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new JMenuItem(SHEET);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ item = new JMenuItem(LABEL);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new JMenuItem(COLOUR);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new JMenuItem(REMOVE);
+ item.addActionListener(this);
+ pop.add(item);
+ pop.show(this, x, y);
+ }
+
+ /**
+ * Action on mouse up is to clear mouse drag data and call mouseReleased on
+ * ScalePanel, to deal with defining the selection group (if any) defined by
+ * the mouse drag
+ *
+ * @param evt
+ */
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (dragMode == DragMode.MatrixSelect)
+ {
+ matrixSelectRange(evt);
+ }
+ graphStretch = -1;
+ mouseDragLastX = -1;
+ mouseDragLastY = -1;
+ firstDragX = -1;
+ firstDragY = -1;
+ mouseDragging = false;
+ if (dragMode == DragMode.Resize)
+ {
+ ap.adjustAnnotationHeight();
+ }
+ dragMode = DragMode.Undefined;
+ if (!matrix_clicked(evt))
+ {
+ ap.getScalePanel().mouseReleased(evt);
+ }
+
+ /*
+ * isPopupTrigger is set in mouseReleased on Windows
+ * (in mousePressed on Mac)
+ */
+ if (evt.isPopupTrigger() && activeRow != -1)
+ {
+ showPopupMenu(evt.getY(), evt.getX());
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseEntered(MouseEvent evt)
+ {
+ this.mouseDragging = false;
+ ap.getScalePanel().mouseEntered(evt);
+ }
+
+ /**
+ * On leaving the panel, calls ScalePanel.mouseExited to deal with scrolling
+ * with column selection on a mouse drag
+ *
+ * @param evt
+ */
+ @Override
+ public void mouseExited(MouseEvent evt)
+ {
+ ap.getScalePanel().mouseExited(evt);
+ }
+
+ /**
+ * Action on starting or continuing a mouse drag. There are two possible
+ * actions:
+ * <ul>
+ * <li>drag up or down on a graphed annotation increases or decreases the
+ * height of the graph</li>
+ * <li>dragging left or right selects the columns dragged across</li>
+ * </ul>
+ * A drag on a graph annotation is treated as column selection if it starts
+ * with more horizontal than vertical movement, and as resize if it starts
+ * with more vertical than horizontal movement. Once started, the drag does
+ * not change mode.
+ *
+ * @param evt
+ */
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ /*
+ * if dragMode is Undefined:
+ * - set to Select if dx > dy
+ * - set to Resize if dy > dx
+ * - do nothing if dx == dy
+ */
+ final int x = evt.getX();
+ final int y = evt.getY();
+ if (dragMode == DragMode.Undefined)
+ {
+ int dx = Math.abs(x - mouseDragLastX);
+ int dy = Math.abs(y - mouseDragLastY);
+ if (graphStretch == -1 || dx > dy)
+ {
+ /*
+ * mostly horizontal drag, or not a graph annotation
+ */
+ dragMode = DragMode.Select;
+ }
+ else if (dy > dx)
+ {
+ /*
+ * mostly vertical drag
+ */
+ dragMode = DragMode.Resize;
+ notJustOne = evt.isShiftDown();
+
+ /*
+ * but could also be a matrix drag
+ */
+ if ((evt.isAltDown() || evt.isAltGraphDown()) && (av.getAlignment()
+ .getAlignmentAnnotation()[graphStretch].graph == AlignmentAnnotation.CONTACT_MAP))
+ {
+ /*
+ * dragging in a matrix
+ */
+ dragMode = DragMode.MatrixSelect;
+ firstDragX = mouseDragLastX;
+ firstDragY = mouseDragLastY;
+ }
+ }
+ }
+
+ if (dragMode == DragMode.Undefined)
+
+ {
+ /*
+ * drag is diagonal - defer deciding whether to
+ * treat as up/down or left/right
+ */
+ return;
+ }
+
+ try
+ {
+ if (dragMode == DragMode.Resize)
+ {
+ /*
+ * resize graph annotation if mouse was dragged up or down
+ */
+ int deltaY = mouseDragLastY - evt.getY();
+ if (deltaY != 0)
+ {
+ AlignmentAnnotation graphAnnotation = av.getAlignment()
+ .getAlignmentAnnotation()[graphStretch];
+ int newHeight = Math.max(0, graphAnnotation.graphHeight + deltaY);
+ if (notJustOne)
+ {
+ for (AlignmentAnnotation similar : av.getAlignment()
+ .findAnnotations(null, graphAnnotation.getCalcId(),
+ graphAnnotation.label))
+ {
+ similar.graphHeight = newHeight;
+ }
+
+ }
+ else
+ {
+ graphAnnotation.graphHeight = newHeight;
+ }
+ adjustPanelHeight();
+ ap.paintAlignment(false, false);
+ }
+ }
+ else if (dragMode == DragMode.MatrixSelect)
+ {
+ /*
+ * TODO draw a rubber band for range
+ */
+ mouseDragLastX = x;
+ mouseDragLastY = y;
+ ap.paintAlignment(false, false);
+ }
+ else
+ {
+ /*
+ * for mouse drag left or right, delegate to
+ * ScalePanel to adjust the column selection
+ */
+ ap.getScalePanel().mouseDragged(evt);
+ }
+ } finally
+ {
+ mouseDragLastX = x;
+ mouseDragLastY = y;
+ }
+ }
+
+ public void matrixSelectRange(MouseEvent evt)
+ {
+ /*
+ * get geometry of drag
+ */
+ int fromY = Math.min(firstDragY, evt.getY());
+ int toY = Math.max(firstDragY, evt.getY());
+ int fromX = Math.min(firstDragX, evt.getX());
+ int toX = Math.max(firstDragX, evt.getX());
+
+ int deltaY = toY - fromY;
+ int deltaX = toX - fromX;
+
+ int[] rowIndex = getRowIndexAndOffset(fromY,
+ av.getAlignment().getAlignmentAnnotation());
+ int[] toRowIndex = getRowIndexAndOffset(toY,
+ av.getAlignment().getAlignmentAnnotation());
+
+ if (rowIndex == null || toRowIndex == null)
+ {
+ jalview.bin.Console.trace("Drag out of range. needs to be clipped");
+
+ }
+ if (rowIndex[0] != toRowIndex[0])
+ {
+ jalview.bin.Console.trace("Drag went to another row. needs to be clipped");
+ }
+
+ // rectangular selection on matrix style annotation
+ AlignmentAnnotation cma = av.getAlignment()
+ .getAlignmentAnnotation()[rowIndex[0]];
+
+ int lastX = getColumnForXPos(fromX);
+ int currentX = getColumnForXPos(toX);
+ int fromXc = Math.min(lastX, currentX);
+ int toXc = Math.max(lastX, currentX);
+ ContactListI forFromX = av.getContactList(cma, fromXc);
+ ContactListI forToX = av.getContactList(cma, toXc);
+
+ if (forFromX != null && forToX != null)
+ {
+ ContactGeometry lastXcgeom = new ContactGeometry(forFromX,
+ cma.graphHeight);
+ ContactGeometry.contactInterval lastXci = lastXcgeom
+ .mapFor(rowIndex[1], rowIndex[1] - deltaY);
+
+ ContactGeometry cXcgeom = new ContactGeometry(forToX,
+ cma.graphHeight);
+ ContactGeometry.contactInterval cXci = cXcgeom.mapFor(rowIndex[1],
+ rowIndex[1] - deltaY);
+
+ // mark rectangular region formed by drag
+ jalview.bin.Console.trace("Matrix Selection from last(" + fromXc
+ + ",[" + lastXci.cStart + "," + lastXci.cEnd + "]) to cur("
+ + toXc + ",[" + cXci.cStart + "," + cXci.cEnd + "])");
+ int fr, to;
+ fr = Math.min(lastXci.cStart, lastXci.cEnd);
+ to = Math.max(lastXci.cStart, lastXci.cEnd);
+ int[] mappedPos = forFromX.getMappedPositionsFor(fr, to);
+ if (mappedPos != null)
+ {
+ jalview.bin.Console.trace("Marking " + fr + " to " + to
+ + " mapping to sequence positions " + mappedPos[0] + " to "
+ + mappedPos[1]);
+ for (int pair = 0; pair < mappedPos.length; pair += 2)
+ {
+ for (int c = mappedPos[pair]; c <= mappedPos[pair + 1]; c++)
+// {
+// if (cma.sequenceRef != null)
+// {
+// int col = cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
+// av.getColumnSelection().addElement(col);
+// }
+// else
+ {
+ av.getColumnSelection().addElement(c);
+ }
+ }
+ }
+ // and again for most recent corner of drag
+ fr = Math.min(cXci.cStart, cXci.cEnd);
+ to = Math.max(cXci.cStart, cXci.cEnd);
+ mappedPos = forFromX.getMappedPositionsFor(fr, to);
+ if (mappedPos != null)
+ {
+ for (int pair = 0; pair < mappedPos.length; pair += 2)
+ {
+ jalview.bin.Console.trace("Marking " + fr + " to " + to
+ + " mapping to sequence positions " + mappedPos[pair] + " to "
+ + mappedPos[pair+1]);
+ for (int c = mappedPos[pair]; c <= mappedPos[pair + 1]; c++)
+ {
+// if (cma.sequenceRef != null)
+// {
+// int col = cma.sequenceRef.findIndex(cma.sequenceRef.getStart()+c);
+// av.getColumnSelection().addElement(col);
+// }
+// else
+ {
+ av.getColumnSelection().addElement(c);
+ }
+ }
+ }
+ }
+ fr = Math.min(lastX, currentX);
+ to = Math.max(lastX, currentX);
+
+ jalview.bin.Console.trace("Marking " + fr + " to " + to);
+ for (int c = fr; c <= to; c++)
+ {
+ av.getColumnSelection().addElement(c);
+ }
+ }
+
+ }
+
+ /**
+ * Constructs the tooltip, and constructs and displays a status message, for
+ * the current mouse position
+ *
+ * @param evt
+ */
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ int yPos = evt.getY();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ int rowAndOffset[] = getRowIndexAndOffset(yPos, aa);
+ int row = rowAndOffset[0];
+
+ if (row == -1)
+ {
+ this.setToolTipText(null);
+ return;
+ }
+
+ int column = getColumnForXPos(evt.getX());
+
+ AlignmentAnnotation ann = aa[row];
+ if (row > -1 && ann.annotations != null
+ && column < ann.annotations.length)
+ {
+ String toolTip = buildToolTip(ann, column, aa, rowAndOffset[1], av,
+ ap);
+ setToolTipText(toolTip == null ? null
+ : JvSwingUtils.wrapTooltip(true, toolTip));
+ String msg = getStatusMessage(av.getAlignment(), column, ann,
+ rowAndOffset[1], av);
+ ap.alignFrame.setStatus(msg);
+ }
+ else
+ {
+ this.setToolTipText(null);
+ ap.alignFrame.setStatus(" ");
+ }
+ }
+
+ private int getColumnForXPos(int x)
+ {
+ int column = (x / av.getCharWidth()) + av.getRanges().getStartRes();
+ column = Math.min(column, av.getRanges().getEndRes());
+
+ if (av.hasHiddenColumns())
+ {
+ column = av.getAlignment().getHiddenColumns()
+ .visibleToAbsoluteColumn(column);
+ }
+ return column;
+ }
+
+ /**
+ * Answers the index in the annotations array of the visible annotation at the
+ * given y position. This is done by adding the heights of visible annotations
+ * until the y position has been exceeded. Answers -1 if no annotations are
+ * visible, or the y position is below all annotations.
+ *
+ * @param yPos
+ * @param aa
+ * @return
+ */
+ static int getRowIndex(int yPos, AlignmentAnnotation[] aa)
+ {
+ if (aa == null)
+ {
+ return -1;
+ }
+ return getRowIndexAndOffset(yPos, aa)[0];
+ }
+
+ static int[] getRowIndexAndOffset(int yPos, AlignmentAnnotation[] aa)
+ {
+ int[] res = new int[2];
+ res[0] = -1;
+ res[1] = 0;
+ if (aa == null)
+ {
+ return res;
+ }
+ int row = -1;
+ int height = 0, lheight = 0;
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].visible)
+ {
+ lheight = height;
+ height += aa[i].height;
+ }
+
+ if (height > yPos)
+ {
+ row = i;
+ res[0] = row;
+ res[1] = height - yPos;
+ break;
+ }
+ }
+ return res;
+ }
+
+ /**
+ * Answers a tooltip for the annotation at the current mouse position, not
+ * wrapped in <html> tags (apply if wanted). Answers null if there is no
+ * tooltip to show.
+ *
+ * @param ann
+ * @param column
+ * @param anns
+ * @param rowAndOffset
+ */
+ static String buildToolTip(AlignmentAnnotation ann, int column,
+ AlignmentAnnotation[] anns, int rowAndOffset, AlignViewportI av,
+ AlignmentPanel ap)
+ {
+ String tooltip = null;
+ if (ann.graphGroup > -1)
+ {
+ StringBuilder tip = new StringBuilder(32);
+ boolean first = true;
+ for (int i = 0; i < anns.length; i++)
+ {
+ if (anns[i].graphGroup == ann.graphGroup
+ && anns[i].annotations[column] != null)
+ {
+ if (!first)
+ {
+ tip.append("<br>");
+ }
+ first = false;
+ tip.append(anns[i].label);
+ String description = anns[i].annotations[column].description;
+ if (description != null && description.length() > 0)
+ {
+ tip.append(" ").append(description);
+ }
+ }
+ }
+ tooltip = first ? null : tip.toString();
+ }
+ else if (column < ann.annotations.length
+ && ann.annotations[column] != null)
+ {
+ tooltip = ann.annotations[column].description;
+ }
+ // TODO abstract tooltip generator so different implementations can be built
+ if (ann.graph == AlignmentAnnotation.CONTACT_MAP)
+ {
+ ContactListI clist = av.getContactList(ann, column);
+ if (clist != null)
+ {
+ ContactGeometry cgeom = new ContactGeometry(clist, ann.graphHeight);
+ ContactGeometry.contactInterval ci = cgeom.mapFor(rowAndOffset);
+ ContactRange cr = clist.getRangeFor(ci.cStart, ci.cEnd);
+ tooltip = "Contact from " + clist.getPosition() + ", [" + ci.cStart
+ + " - " + ci.cEnd + "]" + "<br/>Mean:" + cr.getMean();
+
+ int col = ann.sequenceRef.findPosition(column);
+ int[][] highlightPos;
+ int[] mappedPos = clist.getMappedPositionsFor(ci.cStart, ci.cEnd);
+ if (mappedPos != null)
+ {
+ highlightPos = new int[1 + mappedPos.length][2];
+ highlightPos[0] = new int[] { col, col };
+ for (int p = 0, h = 0; p < mappedPos.length; h++, p += 2)
+ {
+ highlightPos[h][0] = ann.sequenceRef
+ .findPosition(mappedPos[p] - 1);
+ highlightPos[h][1] = ann.sequenceRef
+ .findPosition(mappedPos[p + 1] - 1);
+ }
+ }
+ else
+ {
+ highlightPos = new int[][] { new int[] { col, col } };
+ }
+ ap.getStructureSelectionManager()
+ .highlightPositionsOn(ann.sequenceRef, highlightPos, null);
+ }
+ }
+ return tooltip;
+ }
+
+ /**
+ * Constructs and returns the status bar message
+ *
+ * @param al
+ * @param column
+ * @param ann
+ * @param rowAndOffset
+ */
+ static String getStatusMessage(AlignmentI al, int column,
+ AlignmentAnnotation ann, int rowAndOffset, AlignViewportI av)
+ {
+ /*
+ * show alignment column and annotation description if any
+ */
+ StringBuilder text = new StringBuilder(32);
+ text.append(MessageManager.getString("label.column")).append(" ")
+ .append(column + 1);
+
+ if (column < ann.annotations.length && ann.annotations[column] != null)
+ {
+ String description = ann.annotations[column].description;
+ if (description != null && description.trim().length() > 0)
+ {
+ text.append(" ").append(description);
+ }
+ }
+
+ /*
+ * if the annotation is sequence-specific, show the sequence number
+ * in the alignment, and (if not a gap) the residue and position
+ */
+ SequenceI seqref = ann.sequenceRef;
+ if (seqref != null)
+ {
+ int seqIndex = al.findIndex(seqref);
+ if (seqIndex != -1)
+ {
+ text.append(", ").append(MessageManager.getString("label.sequence"))
+ .append(" ").append(seqIndex + 1);
+ char residue = seqref.getCharAt(column);
+ if (!Comparison.isGap(residue))
+ {
+ text.append(" ");
+ String name;
+ if (al.isNucleotide())
+ {
+ name = ResidueProperties.nucleotideName
+ .get(String.valueOf(residue));
+ text.append(" Nucleotide: ")
+ .append(name != null ? name : residue);
+ }
+ else
+ {
+ name = 'X' == residue ? "X"
+ : ('*' == residue ? "STOP"
+ : ResidueProperties.aa2Triplet
+ .get(String.valueOf(residue)));
+ text.append(" Residue: ").append(name != null ? name : residue);
+ }
+ int residuePos = seqref.findPosition(column);
+ text.append(" (").append(residuePos).append(")");
+ }
+ }
+ }
+
+ return text.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ // if (activeRow != -1)
+ // {
+ // AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ // AlignmentAnnotation anot = aa[activeRow];
+ // }
+ }
+
+ // TODO mouseClicked-content and drawCursor are quite experimental!
+ public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1,
+ int y1)
+ {
+ int pady = av.getCharHeight() / 5;
+ int charOffset = 0;
+ graphics.setColor(Color.black);
+ graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
+
+ if (av.validCharWidth)
+ {
+ graphics.setColor(Color.white);
+
+ char s = seq.getCharAt(res);
+
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s), charOffset + x1,
+ (y1 + av.getCharHeight()) - pady);
+ }
+
+ }
+
+ private volatile boolean imageFresh = false;
+
+ private Rectangle visibleRect = new Rectangle(),
+ clipBounds = new Rectangle();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ */
+ @Override
+ public void paintComponent(Graphics g)
+ {
+
+ // BH: note that this method is generally recommended to
+ // call super.paintComponent(g). Otherwise, the children of this
+ // component will not be rendered. That is not needed here
+ // because AnnotationPanel does not have any children. It is
+ // just a JPanel contained in a JViewPort.
+
+ computeVisibleRect(visibleRect);
+
+ g.setColor(Color.white);
+ g.fillRect(0, 0, visibleRect.width, visibleRect.height);
+
+ if (image != null)
+ {
+ // BH 2018 optimizing generation of new Rectangle().
+ if (fastPaint
+ || (visibleRect.width != (clipBounds = g
+ .getClipBounds(clipBounds)).width)
+ || (visibleRect.height != clipBounds.height))
+ {
+
+ g.drawImage(image, 0, 0, this);
+ fastPaint = false;
+ return;
+ }
+ }
+ imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes()
+ + 1) * av.getCharWidth();
+ if (imgWidth < 1)
+ {
+ return;
+ }
+ Graphics2D gg;
+ if (image == null || imgWidth != image.getWidth(this)
+ || image.getHeight(this) != getHeight())
+ {
+ boolean tried = false;
+ image = null;
+ while (image == null && !tried)
+ {
+ try
+ {
+ image = new BufferedImage(imgWidth,
+ ap.getAnnotationPanel().getHeight(),
+ BufferedImage.TYPE_INT_RGB);
+ tried = true;
+ } catch (IllegalArgumentException exc)
+ {
+ System.err.println(
+ "Serious issue with viewport geometry imgWidth requested was "
+ + imgWidth);
+ return;
+ } catch (OutOfMemoryError oom)
+ {
+ try
+ {
+ System.gc();
+ } catch (Exception x)
+ {
+ }
+ ;
+ new OOMWarning(
+ "Couldn't allocate memory to redraw screen. Please restart Jalview",
+ oom);
+ return;
+ }
+
+ }
+ gg = (Graphics2D) image.getGraphics();
+
+ if (av.antiAlias)
+ {
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
+
+ gg.setFont(av.getFont());
+ fm = gg.getFontMetrics();
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, imgWidth, image.getHeight());
+ imageFresh = true;
+ }
+ else
+ {
+ gg = (Graphics2D) image.getGraphics();
+
+ }
+
+ drawComponent(gg, av.getRanges().getStartRes(),
+ av.getRanges().getEndRes() + 1);
+ gg.dispose();
+ imageFresh = false;
+ g.drawImage(image, 0, 0, this);
+ }
+
+ /**
+ * set true to enable redraw timing debug output on stderr
+ */
+ private final boolean debugRedraw = false;
+
+ /**
+ * non-Thread safe repaint
+ *
+ * @param horizontal
+ * repaint with horizontal shift in alignment
+ */
+ public void fastPaint(int horizontal)
+ {
+ if ((horizontal == 0) || image == null
+ || av.getAlignment().getAlignmentAnnotation() == null
+ || av.getAlignment().getAlignmentAnnotation().length < 1
+ || av.isCalcInProgress())
+ {
+ repaint();
+ return;
+ }
+
+ int sr = av.getRanges().getStartRes();
+ int er = av.getRanges().getEndRes() + 1;
+ int transX = 0;
+
+ Graphics2D gg = (Graphics2D) image.getGraphics();
+
+ if (imgWidth > Math.abs(horizontal * av.getCharWidth()))
+ {
+ // scroll is less than imgWidth away so can re-use buffered graphics
+ gg.copyArea(0, 0, imgWidth, getHeight(),
+ -horizontal * av.getCharWidth(), 0);
+
+ if (horizontal > 0) // scrollbar pulled right, image to the left
+ {
+ transX = (er - sr - horizontal) * av.getCharWidth();
+ sr = er - horizontal;
+ }
+ else if (horizontal < 0)
+ {
+ er = sr - horizontal;
+ }
+ }
+ gg.translate(transX, 0);
+
+ drawComponent(gg, sr, er);
+
+ gg.translate(-transX, 0);
+
+ gg.dispose();
+
+ fastPaint = true;
+
+ // Call repaint on alignment panel so that repaints from other alignment
+ // panel components can be aggregated. Otherwise performance of the overview
+ // window and others may be adversely affected.
+ av.getAlignPanel().repaint();
+ }
+
+ private volatile boolean lastImageGood = false;
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
+ * @param endRes
+ * DOCUMENT ME!
+ */
+ public void drawComponent(Graphics g, int startRes, int endRes)
+ {
+ BufferedImage oldFaded = fadedImage;
+ if (av.isCalcInProgress())
+ {
+ if (image == null)
+ {
+ lastImageGood = false;
+ return;
+ }
+ // We'll keep a record of the old image,
+ // and draw a faded image until the calculation
+ // has completed
+ if (lastImageGood
+ && (fadedImage == null || fadedImage.getWidth() != imgWidth
+ || fadedImage.getHeight() != image.getHeight()))
+ {
+ // System.err.println("redraw faded image ("+(fadedImage==null ?
+ // "null image" : "") + " lastGood="+lastImageGood+")");
+ fadedImage = new BufferedImage(imgWidth, image.getHeight(),
+ BufferedImage.TYPE_INT_RGB);
+
+ Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
+
+ fadedG.setColor(Color.white);
+ fadedG.fillRect(0, 0, imgWidth, image.getHeight());
+
+ fadedG.setComposite(
+ AlphaComposite.getInstance(AlphaComposite.SRC_OVER, .3f));
+ fadedG.drawImage(image, 0, 0, this);
+
+ }
+ // make sure we don't overwrite the last good faded image until all
+ // calculations have finished
+ lastImageGood = false;
+
+ }
+ else
+ {
+ if (fadedImage != null)
+ {
+ oldFaded = fadedImage;
+ }
+ fadedImage = null;
+ }
+
+ g.setColor(Color.white);
+ g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight());
+
+ g.setFont(av.getFont());
+ if (fm == null)
+ {
+ fm = g.getFontMetrics();
+ }
+
+ if ((av.getAlignment().getAlignmentAnnotation() == null)
+ || (av.getAlignment().getAlignmentAnnotation().length < 1))
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getWidth(), getHeight());
+ g.setColor(Color.black);
+ if (av.validCharWidth)
+ {
+ g.drawString(MessageManager
+ .getString("label.alignment_has_no_annotations"), 20, 15);
+ }
+
+ return;
+ }
+ lastImageGood = renderer.drawComponent(this, av, g, activeRow, startRes,
+ endRes);
+ if (!lastImageGood && fadedImage == null)
+ {
+ fadedImage = oldFaded;
+ }
+ if (dragMode == DragMode.MatrixSelect)
+ {
+ g.setColor(Color.yellow);
+ g.drawRect(Math.min(firstDragX, mouseDragLastX),
+ Math.min(firstDragY, mouseDragLastY),
+ Math.max(firstDragX, mouseDragLastX)
+ - Math.min(firstDragX, mouseDragLastX),
+ Math.max(firstDragY, mouseDragLastY)
+ - Math.min(firstDragY, mouseDragLastY));
+
+ }
+ }
+
+ @Override
+ public FontMetrics getFontMetrics()
+ {
+ return fm;
+ }
+
+ @Override
+ public Image getFadedImage()
+ {
+ return fadedImage;
+ }
+
+ @Override
+ public int getFadedImageWidth()
+ {
+ return imgWidth;
+ }
+
+ private int[] bounds = new int[2];
+
+ @Override
+ public int[] getVisibleVRange()
+ {
+ if (ap != null && ap.getAlabels() != null)
+ {
+ int sOffset = -ap.getAlabels().getScrollOffset();
+ int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
+ bounds[0] = sOffset;
+ bounds[1] = visHeight;
+ return bounds;
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ /**
+ * Try to ensure any references held are nulled
+ */
+ public void dispose()
+ {
+ av = null;
+ ap = null;
+ image = null;
+ fadedImage = null;
+ // gg = null;
+ _mwl = null;
+
+ /*
+ * I created the renderer so I will dispose of it
+ */
+ if (renderer != null)
+ {
+ renderer.dispose();
+ }
+ }
+
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // Respond to viewport range changes (e.g. alignment panel was scrolled)
+ // Both scrolling and resizing change viewport ranges: scrolling changes
+ // both start and end points, but resize only changes end values.
+ // Here we only want to fastpaint on a scroll, with resize using a normal
+ // paint, so scroll events are identified as changes to the horizontal or
+ // vertical start value.
+ if (evt.getPropertyName().equals(ViewportRanges.STARTRES))
+ {
+ fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
+ }
+ else if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ))
+ {
+ fastPaint(((int[]) evt.getNewValue())[0]
+ - ((int[]) evt.getOldValue())[0]);
+ }
+ else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT))
+ {
+ repaint();
+ }
+ }
+
+ /**
+ * computes the visible height of the annotation panel
+ *
+ * @param adjustPanelHeight
+ * - when false, just adjust existing height according to other
+ * windows
+ * @param annotationHeight
+ * @return height to use for the ScrollerPreferredVisibleSize
+ */
+ public int adjustForAlignFrame(boolean adjustPanelHeight,
+ int annotationHeight)
+ {
+ /*
+ * Estimate available height in the AlignFrame for alignment +
+ * annotations. Deduct an estimate for title bar, menu bar, scale panel,
+ * hscroll, status bar, insets.
+ */
+ int stuff = (ap.getViewName() != null ? 30 : 0)
+ + (Platform.isAMacAndNotJS() ? 120 : 140);
+ int availableHeight = ap.alignFrame.getHeight() - stuff;
+ int rowHeight = av.getCharHeight();
+
+ if (adjustPanelHeight)
+ {
+ int alignmentHeight = rowHeight * av.getAlignment().getHeight();
+
+ /*
+ * 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 = Math.min(ap.annotationScroller.getSize().height,
+ availableHeight - 2 * rowHeight);
+ }
+ return annotationHeight;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff