-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-package jalview.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class AnnotationPanel\r
- extends Panel implements AdjustmentListener\r
-{\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- int activeRow = -1;\r
-\r
- Vector 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
- Image image;\r
- Graphics gg;\r
- FontMetrics fm;\r
- int imgWidth = 0;\r
-\r
- boolean fastPaint = false;\r
-\r
- public static int GRAPH_HEIGHT = 40;\r
-\r
- public AnnotationPanel(AlignmentPanel ap)\r
- {\r
- this.ap = ap;\r
- av = ap.av;\r
- this.setLayout(null);\r
- adjustPanelHeight();\r
-\r
- addMouseMotionListener(new MouseMotionAdapter()\r
- {\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- doMouseMoved(evt);\r
- }\r
- });\r
-\r
- // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );\r
- }\r
-\r
-\r
- public AnnotationPanel(AlignViewport av)\r
- {\r
- this.av = av;\r
- }\r
-\r
-\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
- {\r
- ap.alabels.setScrollOffset( -evt.getValue());\r
- }\r
-\r
- public int adjustPanelHeight()\r
- {\r
- // setHeight of panels\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
-\r
-\r
- int height = 0;\r
- if (aa != null)\r
- {\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- if (!aa[i].visible)\r
- {\r
- continue;\r
- }\r
-\r
- aa[i].height = 0;\r
-\r
- if (aa[i].hasText)\r
- {\r
- aa[i].height += av.charHeight;\r
- }\r
- if (aa[i].hasIcons)\r
- {\r
- aa[i].height += 16;\r
- }\r
-\r
- if (aa[i].graph>0)\r
- {\r
- aa[i].height += GRAPH_HEIGHT;\r
- }\r
-\r
- if (aa[i].height == 0)\r
- {\r
- aa[i].height = 20;\r
- }\r
- height += aa[i].height;\r
- }\r
- }\r
- else\r
- {\r
- height = 20;\r
- }\r
-\r
- this.setSize(getSize().width, height);\r
- if(ap!=null)\r
- ap.annotationScroller.setSize(getSize().width, height);\r
-\r
-\r
- repaint();\r
-\r
- return height;\r
-\r
- }\r
-\r
- public void addEditableColumn(int i)\r
- {\r
- if (activeRow == -1)\r
- {\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
- if(aa ==null)\r
- return;\r
-\r
- for (int j = 0; j < aa.length; j++)\r
- {\r
- if (aa[j].editable)\r
- {\r
- activeRow = j;\r
- break;\r
- }\r
- }\r
- }\r
-\r
- if (activeRes == null)\r
- {\r
- activeRes = new Vector();\r
- activeRes.addElement(String.valueOf(i));\r
- return;\r
- }\r
-\r
- activeRes.addElement(String.valueOf(i));\r
- }\r
-\r
- public void doMouseMoved(MouseEvent evt)\r
- {\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
- if (aa == null)\r
- {\r
- return;\r
- }\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
- {\r
- height += aa[i].height;\r
- }\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
- 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
- public void update(Graphics g)\r
- {\r
- paint(g);\r
- }\r
-\r
- public void paint(Graphics g)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0,0, getSize().width, getSize().height);\r
- imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
-\r
- if (image == null || imgWidth != image.getWidth(this))\r
- {\r
- image = createImage(imgWidth, ap.annotationPanel.getSize().height);\r
- gg = image.getGraphics();\r
- gg.setFont(av.getFont());\r
- fm = gg.getFontMetrics();\r
- fastPaint = false;\r
- }\r
-\r
- if (fastPaint)\r
- {\r
- g.drawImage(image, 0, 0, this);\r
- fastPaint = false;\r
- return;\r
- }\r
-\r
- drawComponent(gg, av.startRes, av.endRes + 1);\r
- g.drawImage(image, 0, 0, this);\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, getSize().height, -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
- 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
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- * @param startRes DOCUMENT ME!\r
- * @param endRes DOCUMENT ME!\r
- */\r
- public void drawComponent(Graphics g, int startRes, int endRes)\r
- {\r
- g.setFont(av.getFont());\r
-\r
- if (fm == null)\r
- fm = g.getFontMetrics();\r
-\r
-\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);\r
-\r
- if ((av.alignment.getAlignmentAnnotation() == null) ||\r
- (av.alignment.getAlignmentAnnotation().length < 1))\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, getSize().width, getSize().height);\r
- g.setColor(Color.black);\r
- g.drawString("Alignment has no annotations", 20, 15);\r
-\r
- return;\r
- }\r
-\r
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
-\r
- int j;\r
- int x = 0;\r
- int 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
-\r
- boolean [] graphGroupDrawn = new boolean[aa.length];\r
-\r
-\r
- //\u03B2 \u03B1\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- AlignmentAnnotation row = aa[i];\r
-\r
- if (!row.visible)\r
- {\r
- continue;\r
- }\r
-\r
-\r
-\r
- if (row.graph>0)\r
- {\r
- if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )\r
- continue;\r
-\r
- // this is so that we draw the characters below the graph\r
- y += row.height;\r
-\r
- if (row.hasText)\r
- {\r
- y -= av.charHeight;\r
- }\r
- }\r
-\r
- if (row.hasText)\r
- {\r
- iconOffset = av.charHeight / 2;\r
- }\r
- else\r
- {\r
- iconOffset = 0;\r
- }\r
-\r
- for (j = startRes; j < endRes; j++)\r
- {\r
- if ((row.annotations.length <= j) ||\r
- (row.annotations[j] == null))\r
- {\r
- validRes = false;\r
- }\r
- else\r
- {\r
- validRes = true;\r
- }\r
-\r
- x = (j - startRes) * av.charWidth;\r
-\r
- if (activeRow == i)\r
- {\r
- g.setColor(Color.red);\r
-\r
- if (activeRes != null)\r
- {\r
- for (int n = 0; n < activeRes.size(); n++)\r
- {\r
- int v = Integer.parseInt(activeRes.elementAt(n).toString());\r
-\r
- if (v == j)\r
- {\r
- g.fillRect((j - startRes) * av.charWidth, y,\r
- av.charWidth, row.height);\r
- }\r
- }\r
- }\r
- }\r
-\r
- if (validRes &&\r
- (row.annotations[j].displayCharacter.length() > 0))\r
- {\r
-\r
- int charOffset = (av.charWidth -\r
- fm.charWidth(row.annotations[j].displayCharacter.charAt(\r
- 0))) / 2;\r
- g.setColor(row.annotations[j].colour);\r
-\r
- if (j == 0 || row.graph>0)\r
- {\r
- g.drawString(row.annotations[j].displayCharacter, x+charOffset,\r
- y + iconOffset + 3);\r
- }\r
- else if (((row.annotations[j - 1] == null) ||\r
- (row.annotations[j].displayCharacter != row.annotations[j -\r
- 1].displayCharacter)))\r
- {\r
- g.drawString(row.annotations[j].displayCharacter, x+charOffset,\r
- y + iconOffset + 3);\r
- }\r
- }\r
-\r
- if (row.hasIcons)\r
- {\r
- if (!validRes ||\r
- (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,\r
- x - lastSSX[i], 7, 8, 8);\r
-\r
- break;\r
-\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i] - 4, 7);\r
- g.fillPolygon(new int[] { x - 4, x - 4, x },\r
- new int[]\r
- {\r
- y + iconOffset, y + 14 + iconOffset,\r
- y + 8 + iconOffset\r
- }, 3);\r
-\r
- break;\r
-\r
-\r
- default:\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y + 6 + iconOffset,\r
- x - lastSSX[i], 2);\r
-\r
- break;\r
- }\r
-\r
- if (validRes)\r
- {\r
- lastSS[i] = row.annotations[j].secondaryStructure;\r
- }\r
- else\r
- {\r
- lastSS[i] = ' ';\r
- }\r
-\r
- lastSSX[i] = x;\r
- }\r
- }\r
- }\r
-\r
- x += av.charWidth;\r
-\r
- if (row.hasIcons)\r
- {\r
- switch (lastSS[i])\r
- {\r
- case 'H':\r
- g.setColor(HELIX_COLOUR);\r
- g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i], 7, 8, 8);\r
-\r
- break;\r
-\r
- case 'E':\r
- g.setColor(SHEET_COLOUR);\r
-\r
- if (row.annotations.length > endRes\r
- && row.annotations[endRes].secondaryStructure != 'E')\r
- {\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i] - 4, 7);\r
- g.fillPolygon(new int[]\r
- {x - 4, x - 4, x},\r
- new int[]\r
- {\r
- y + iconOffset, y + 14 + iconOffset,\r
- y + 7 + iconOffset\r
- }, 3);\r
- }\r
- else\r
- g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
- x - lastSSX[i], 7);\r
-\r
- break;\r
-\r
- case 'C':\r
- break;\r
-\r
- default:\r
- g.setColor(Color.gray);\r
- g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);\r
-\r
- break;\r
- }\r
- }\r
-\r
- if (row.graph>0)\r
- {\r
- if(row.graph == AlignmentAnnotation.LINE_GRAPH )\r
- {\r
- if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])\r
- {\r
- float groupmax=-999999, groupmin=9999999;\r
- for(int gg=0; gg<aa.length; gg++)\r
- {\r
- if(aa[gg].graphGroup!=row.graphGroup)\r
- continue;\r
-\r
- if(aa[gg]!=row)\r
- aa[gg].visible = false;\r
-\r
- if(aa[gg].graphMax>groupmax)\r
- groupmax = aa[gg].graphMax;\r
- if(aa[gg].graphMin<groupmin)\r
- groupmin = aa[gg].graphMin;\r
- }\r
-\r
- for (int gg = 0; gg < aa.length; gg++)\r
- {\r
- if (aa[gg].graphGroup == row.graphGroup)\r
- {\r
- drawLineGraph(g, aa[gg], startRes, endRes, y,\r
- groupmin, groupmax,\r
- row.graphHeight);\r
- }\r
- }\r
-\r
- graphGroupDrawn[ row.graphGroup ] = true;\r
- }\r
- else\r
- drawLineGraph(g, row, startRes, endRes,\r
- y, row.graphMin, row.graphMax, row.graphHeight );\r
- }\r
- else if(row.graph == AlignmentAnnotation.BAR_GRAPH )\r
- drawBarGraph(g, row, startRes, endRes,\r
- row.graphMin, row.graphMax, y);\r
- }\r
-\r
- if (row.graph>0 && row.hasText)\r
- {\r
- y += av.charHeight;\r
- }\r
-\r
- if (row.graph==0)\r
- {\r
- y += aa[i].height;\r
- }\r
- }\r
- }\r
-\r
- public void drawLineGraph(Graphics g, AlignmentAnnotation aa,\r
- int sRes, int eRes,\r
- int y,\r
- float min, float max,\r
- int graphHeight)\r
- {\r
- if(sRes>aa.annotations.length)\r
- return;\r
-\r
-\r
- eRes = Math.min(eRes, aa.annotations.length);\r
-\r
- int x = 0;\r
-\r
- //Adjustment for fastpaint to left\r
- if(eRes<av.endRes)\r
- eRes++;\r
-\r
- if(sRes==0)\r
- {\r
- sRes++;\r
- x+=av.charWidth;\r
- }\r
-\r
- int y1=y, y2=y;\r
- float range = max - min;\r
-\r
- ////Draw origin\r
- if(min<0)\r
- y2 = (int)(y - (0-min / range)*graphHeight);\r
-\r
- g.setColor(Color.gray);\r
- g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);\r
-\r
-\r
- if(aa.threshold!=null)\r
- {\r
- g.setColor(aa.threshold.colour);\r
- y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);\r
- g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);\r
- }\r
-\r
- for (int j = sRes; j < eRes; j++)\r
- {\r
- if(aa.annotations[j]==null || aa.annotations[j-1]==null)\r
- {\r
- x+=av.charWidth;\r
- continue;\r
- }\r
- g.setColor(aa.annotations[j].colour);\r
- y1 = y - (int) (((aa.annotations[j-1].value-min) / range) * graphHeight);\r
- y2 = y - (int) (((aa.annotations[j].value-min) / range) * graphHeight);\r
- g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
- x += av.charWidth;\r
- }\r
- }\r
-\r
- public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\r
- int sRes, int eRes,\r
- float min, float max,\r
- int y)\r
- {\r
- if(sRes>aa.annotations.length)\r
- return;\r
-\r
-\r
- eRes = Math.min(eRes, aa.annotations.length);\r
-\r
- int x=0, y1, y2;\r
-\r
- float range = max - min;\r
-\r
- if(aa.threshold!=null)\r
- {\r
- g.setColor(aa.threshold.colour);\r
- y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);\r
- g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);\r
- }\r
-\r
- y1 = y2 = y;\r
-\r
- if(min<0)\r
- y2 = (int)(y - (0-min / (range))*aa.graphHeight);\r
-\r
- g.setColor(Color.gray);\r
-\r
- g.drawLine(x,y2,(eRes-sRes+1)*av.charWidth,y2);\r
-\r
- for (int j = sRes; j < eRes; j++)\r
- {\r
-\r
- if (aa.annotations[j] == null)\r
- {\r
- x += av.charWidth;\r
- continue;\r
- }\r
-\r
- g.setColor(aa.annotations[j].colour);\r
- y1 = y - (int) (((aa.annotations[j].value-min) / (range)) * aa.graphHeight);\r
-\r
- if(y1-y2>0)\r
- g.fillRect(x, y2, av.charWidth, y1-y2 );\r
- else\r
- g.fillRect(x, y1, av.charWidth, y2-y1 );\r
-\r
- x += av.charWidth;\r
- }\r
-\r
- }\r
-\r
- // used by overview window\r
- public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)\r
- {\r
- g.setColor(Color.white);\r
- g.fillRect(0, 0, width, y);\r
- g.setColor(new Color(0, 0, 180));\r
-\r
- int x = 0, height;\r
-\r
- for (int j = sRes; j < eRes; j++)\r
- {\r
- g.setColor(aa.annotations[j].colour);\r
-\r
- height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);\r
- if(height>y)\r
- height = y;\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 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.AwtRenderPanelI;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
+public class AnnotationPanel extends Panel implements AwtRenderPanelI,
+ AdjustmentListener, ActionListener, MouseListener,
+ MouseMotionListener
+{
+ AlignViewport av;
+
+ AlignmentPanel ap;
+
+ int activeRow = -1;
+
+ final String HELIX = "Helix";
+
+ final String SHEET = "Sheet";
+
+ /**
+ * For RNA secondary structure "stems" aka helices
+ */
+ final String STEM = "RNA Helix";
+
+ final String LABEL = "Label";
+
+ final String REMOVE = "Remove Annotation";
+
+ final String COLOUR = "Colour";
+
+ final Color HELIX_COLOUR = Color.red.darker();
+
+ final Color SHEET_COLOUR = Color.green.darker().darker();
+
+ Image image;
+
+ Graphics gg;
+
+ FontMetrics fm;
+
+ int imgWidth = 0;
+
+ boolean fastPaint = false;
+
+ // Used For mouse Dragging and resizing graphs
+ int graphStretch = -1;
+
+ int graphStretchY = -1;
+
+ boolean mouseDragging = false;
+
+ public static int GRAPH_HEIGHT = 40;
+
+ boolean MAC = false;
+
+ public final AnnotationRenderer renderer;
+
+ public AnnotationPanel(AlignmentPanel ap)
+ {
+ MAC = new jalview.util.Platform().isAMac();
+ this.ap = ap;
+ av = ap.av;
+ setLayout(null);
+ int height = adjustPanelHeight();
+ ap.apvscroll.setValues(0, getSize().height, 0, height);
+
+ addMouseMotionListener(this);
+
+ addMouseListener(this);
+
+ // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
+ renderer = new AnnotationRenderer();
+ }
+
+ public AnnotationPanel(AlignViewport av)
+ {
+ this.av = av;
+ renderer = new AnnotationRenderer();
+ }
+
+ @Override
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ }
+
+ /**
+ * 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 label = "";
+ if (av.getColumnSelection() != null
+ && av.getColumnSelection().size() > 0
+ && anot[av.getColumnSelection().getMin()] != null)
+ {
+ label = anot[av.getColumnSelection().getMin()].displayCharacter;
+ }
+
+ if (evt.getActionCommand().equals(REMOVE))
+ {
+ for (int i = 0; i < av.getColumnSelection().size(); i++)
+ {
+ anot[av.getColumnSelection().columnAt(i)] = null;
+ }
+ }
+ else if (evt.getActionCommand().equals(LABEL))
+ {
+ label = enterLabel(label, "Enter Label");
+
+ if (label == null)
+ {
+ return;
+ }
+
+ if ((label.length() > 0) && !aa[activeRow].hasText)
+ {
+ aa[activeRow].hasText = true;
+ }
+
+ for (int i = 0; i < av.getColumnSelection().size(); i++)
+ {
+ int index = av.getColumnSelection().columnAt(i);
+
+ if (!av.getColumnSelection().isVisible(index))
+ {
+ continue;
+ }
+
+ if (anot[index] == null)
+ {
+ anot[index] = new Annotation(label, "", ' ', 0);
+ }
+
+ anot[index].displayCharacter = label;
+ }
+ }
+ else if (evt.getActionCommand().equals(COLOUR))
+ {
+ UserDefinedColours udc = new UserDefinedColours(this, Color.black,
+ ap.alignFrame);
+
+ Color col = udc.getColor();
+
+ for (int i = 0; i < av.getColumnSelection().size(); i++)
+ {
+ int index = av.getColumnSelection().columnAt(i);
+
+ if (!av.getColumnSelection().isVisible(index))
+ {
+ continue;
+ }
+
+ if (anot[index] == null)
+ {
+ anot[index] = new Annotation("", "", ' ', 0);
+ }
+
+ anot[index].colour = col;
+ }
+ }
+ else
+ // HELIX OR SHEET
+ {
+ char type = 0;
+ String symbol = "\u03B1";
+
+ if (evt.getActionCommand().equals(HELIX))
+ {
+ type = 'H';
+ }
+ else if (evt.getActionCommand().equals(SHEET))
+ {
+ type = 'E';
+ symbol = "\u03B2";
+ }
+
+ // Added by LML to color stems
+ else if (evt.getActionCommand().equals(STEM))
+ {
+ type = 'S';
+ symbol = "\u03C3";
+ }
+
+ if (!aa[activeRow].hasIcons)
+ {
+ aa[activeRow].hasIcons = true;
+ }
+
+ label = enterLabel(symbol, "Enter Label");
+
+ if (label == null)
+ {
+ return;
+ }
+
+ if ((label.length() > 0) && !aa[activeRow].hasText)
+ {
+ aa[activeRow].hasText = true;
+ if (evt.getActionCommand().equals(STEM))
+ {
+ aa[activeRow].showAllColLabels = true;
+ }
+ }
+
+ for (int i = 0; i < av.getColumnSelection().size(); i++)
+ {
+ int index = av.getColumnSelection().columnAt(i);
+
+ if (!av.getColumnSelection().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();
+ adjustPanelHeight();
+ repaint();
+
+ return;
+ }
+
+ String enterLabel(String text, String label)
+ {
+ EditNameDialog dialog = new EditNameDialog(text, null, label, null,
+ ap.alignFrame, "Enter Label", 400, 200, true);
+
+ if (dialog.accept)
+ {
+ return dialog.getName();
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ if (aa == null)
+ {
+ return;
+ }
+
+ int height = -scrollOffset;
+ activeRow = -1;
+
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].visible)
+ {
+ height += aa[i].height;
+ }
+
+ if (evt.getY() < height)
+ {
+ if (aa[i].editable)
+ {
+ activeRow = i;
+ }
+ else if (aa[i].graph > 0)
+ {
+ // Stretch Graph
+ graphStretch = i;
+ graphStretchY = evt.getY();
+ }
+
+ break;
+ }
+ }
+
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK
+ && activeRow != -1)
+ {
+ if (av.getColumnSelection() == null)
+ {
+ return;
+ }
+
+ PopupMenu pop = new PopupMenu(
+ MessageManager.getString("label.structure_type"));
+ MenuItem item;
+ /*
+ * Just display the needed structure options
+ */
+ if (av.getAlignment().isNucleotide() == true)
+ {
+ item = new MenuItem(STEM);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ else
+ {
+ item = new MenuItem(HELIX);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new MenuItem(SHEET);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ item = new MenuItem(LABEL);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new MenuItem(COLOUR);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new MenuItem(REMOVE);
+ item.addActionListener(this);
+ pop.add(item);
+ ap.alignFrame.add(pop);
+ pop.show(this, evt.getX(), evt.getY());
+
+ return;
+ }
+
+ ap.scalePanel.mousePressed(evt);
+ }
+
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ graphStretch = -1;
+ graphStretchY = -1;
+ mouseDragging = false;
+ if (needValidating)
+ {
+ ap.validate();
+ needValidating = false;
+ }
+ ap.scalePanel.mouseReleased(evt);
+ }
+
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ }
+
+ boolean needValidating = false;
+
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ if (graphStretch > -1)
+ {
+ av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+ - evt.getY();
+ if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+ {
+ av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+ }
+ graphStretchY = evt.getY();
+ av.calcPanelHeight();
+ needValidating = true;
+ ap.paintAlignment(true);
+ }
+ else
+ {
+ ap.scalePanel.mouseDragged(evt);
+ }
+ }
+
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ if (aa == null)
+ {
+ return;
+ }
+
+ int row = -1;
+ int height = -scrollOffset;
+ for (int i = 0; i < aa.length; i++)
+ {
+
+ if (aa[i].visible)
+ {
+ height += aa[i].height;
+ }
+
+ if (evt.getY() < height)
+ {
+ row = i;
+ break;
+ }
+ }
+
+ int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+
+ if (av.hasHiddenColumns())
+ {
+ res = av.getColumnSelection().adjustForHiddenColumns(res);
+ }
+
+ if (row > -1 && res < aa[row].annotations.length
+ && aa[row].annotations[res] != null)
+ {
+ StringBuffer text = new StringBuffer("Sequence position " + (res + 1));
+ if (aa[row].annotations[res].description != null)
+ {
+ text.append(" " + aa[row].annotations[res].description);
+ }
+ ap.alignFrame.statusBar.setText(text.toString());
+ }
+ }
+
+ @Override
+ public void mouseEntered(MouseEvent evt)
+ {
+ ap.scalePanel.mouseEntered(evt);
+ }
+
+ @Override
+ public void mouseExited(MouseEvent evt)
+ {
+ ap.scalePanel.mouseExited(evt);
+ }
+
+ public int adjustPanelHeight()
+ {
+ return adjustPanelHeight(true);
+ }
+
+ public int adjustPanelHeight(boolean repaint)
+ {
+ int height = av.calcPanelHeight();
+ this.setSize(new Dimension(getSize().width, height));
+ if (repaint)
+ {
+ repaint();
+ }
+ return height;
+ }
+
+ /**
+ * calculate the height for visible annotation, revalidating bounds where
+ * necessary ABSTRACT GUI METHOD
+ *
+ * @return total height of annotation
+ */
+
+ public void addEditableColumn(int i)
+ {
+ if (activeRow == -1)
+ {
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ if (aa == null)
+ {
+ return;
+ }
+
+ for (int j = 0; j < aa.length; j++)
+ {
+ if (aa[j].editable)
+ {
+ activeRow = j;
+ break;
+ }
+ }
+ }
+ }
+
+ @Override
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
+
+ @Override
+ public void paint(Graphics g)
+ {
+ Dimension d = getSize();
+ imgWidth = d.width;
+ // (av.endRes - av.startRes + 1) * av.charWidth;
+ if (imgWidth < 1 || d.height < 1)
+ {
+ return;
+ }
+ if (image == null || imgWidth != image.getWidth(this)
+ || d.height != image.getHeight(this))
+ {
+ image = createImage(imgWidth, d.height);
+ gg = image.getGraphics();
+ gg.setFont(av.getFont());
+ fm = gg.getFontMetrics();
+ fastPaint = false;
+ }
+
+ if (fastPaint)
+ {
+ g.drawImage(image, 0, 0, this);
+ fastPaint = false;
+ return;
+ }
+
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, getSize().width, getSize().height);
+ drawComponent(gg, av.startRes, av.endRes + 1);
+
+ g.drawImage(image, 0, 0, this);
+ }
+
+ public void fastPaint(int horizontal)
+ {
+ if (horizontal == 0
+ || av.getAlignment().getAlignmentAnnotation() == null
+ || av.getAlignment().getAlignmentAnnotation().length < 1)
+ {
+ repaint();
+ return;
+ }
+
+ gg.copyArea(0, 0, imgWidth, getSize().height,
+ -horizontal * av.getCharWidth(), 0);
+ int sr = av.startRes, er = av.endRes + 1, transX = 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);
+
+ fastPaint = true;
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
+ * @param endRes
+ * DOCUMENT ME!
+ */
+ public void drawComponent(Graphics g, int startRes, int endRes)
+ {
+ Font ofont = av.getFont();
+ g.setFont(ofont);
+
+ g.setColor(Color.white);
+ g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(),
+ getSize().height);
+
+ if (fm == null)
+ {
+ fm = g.getFontMetrics();
+ }
+
+ if ((av.getAlignment().getAlignmentAnnotation() == null)
+ || (av.getAlignment().getAlignmentAnnotation().length < 1))
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getSize().width, getSize().height);
+ g.setColor(Color.black);
+ if (av.validCharWidth)
+ {
+ g.drawString(MessageManager
+ .getString("label.alignment_has_no_annotations"), 20, 15);
+ }
+
+ return;
+ }
+ g.translate(0, -scrollOffset);
+ renderer.drawComponent(this, av, g, activeRow, startRes, endRes);
+ g.translate(0, +scrollOffset);
+ }
+
+ int scrollOffset = 0;
+
+ public void setScrollOffset(int value, boolean repaint)
+ {
+ scrollOffset = value;
+ if (repaint)
+ {
+ repaint();
+ }
+ }
+
+ @Override
+ public FontMetrics getFontMetrics()
+ {
+ return fm;
+ }
+
+ @Override
+ public Image getFadedImage()
+ {
+ return image;
+ }
+
+ @Override
+ public int getFadedImageWidth()
+ {
+ return imgWidth;
+ }
+
+ private int[] bounds = new int[2];
+
+ @Override
+ public int[] getVisibleVRange()
+ {
+ if (ap != null && ap.alabels != null)
+ {
+ int sOffset = -ap.alabels.scrollOffset;
+ int visHeight = sOffset + ap.annotationPanelHolder.getHeight();
+ bounds[0] = sOffset;
+ bounds[1] = visHeight;
+ return bounds;
+ }
+ else
+ {
+ return null;
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff