/*\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
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
import java.awt.*;\r
-import java.awt.Graphics2D.*;\r
import java.awt.image.*;\r
import javax.swing.*;\r
+\r
import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-public class IdCanvas extends JPanel\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class IdCanvas\r
+ extends JPanel\r
{\r
protected AlignViewport av;\r
-\r
- protected boolean showScores = true;\r
-\r
- protected int maxIdLength = -1;\r
- protected String maxIdStr = null;\r
+ protected boolean showScores = true;\r
+ protected int maxIdLength = -1;\r
+ protected String maxIdStr = null;\r
BufferedImage image;\r
Graphics2D gg;\r
- int imgHeight=0;\r
+ int imgHeight = 0;\r
boolean fastPaint = false;\r
-\r
java.util.Vector searchResults;\r
-\r
+ FontMetrics fm;\r
+ AnnotationLabels labels = null;\r
+ AnnotationPanel ap;\r
+ Font idfont;\r
+\r
+ /**\r
+ * Creates a new IdCanvas object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ */\r
public IdCanvas(AlignViewport av)\r
{\r
setLayout(new BorderLayout());\r
- this.av = av;\r
- PaintRefresher.Register(this);\r
+ this.av = av;\r
+ PaintRefresher.Register(this, av.getSequenceSetId());\r
}\r
\r
- public void drawIdString(Graphics2D gg,SequenceI s,int i, int starty, int ypos) {\r
- int charHeight = av.getCharHeight();\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param gg DOCUMENT ME!\r
+ * @param s DOCUMENT ME!\r
+ * @param i DOCUMENT ME!\r
+ * @param starty DOCUMENT ME!\r
+ * @param ypos DOCUMENT ME!\r
+ */\r
+ public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty,\r
+ int ypos)\r
+ {\r
+ int xPos = 0;\r
+ int panelWidth = getWidth();\r
+ int charHeight = av.charHeight;\r
\r
- if(searchResults!=null && searchResults.contains(s))\r
- {\r
- gg.setColor(Color.black);\r
- gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);\r
- gg.setColor(Color.white);\r
- }\r
- else if (av.getSelectionGroup()!=null && av.getSelectionGroup().sequences.contains(s)) {\r
- gg.setColor(Color.lightGray);\r
- gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);\r
- gg.setColor(Color.white);\r
- } else {\r
- gg.setColor(s.getColor());\r
- gg.fillRect(0,AlignmentUtil.getPixelHeight(starty,i,charHeight)+ ypos,getWidth(),charHeight);\r
- gg.setColor(Color.black);\r
- }\r
+ if ( (searchResults != null) && searchResults.contains(s))\r
+ {\r
+ gg.setColor(Color.black);\r
+ gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),\r
+ charHeight);\r
+ gg.setColor(Color.white);\r
+ }\r
+ else if ( (av.getSelectionGroup() != null) &&\r
+ av.getSelectionGroup().getSequences(null).contains(s))\r
+ {\r
+ gg.setColor(Color.lightGray);\r
+ gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),\r
+ charHeight);\r
+ gg.setColor(Color.white);\r
+ }\r
+ else\r
+ {\r
+ gg.setColor(av.getSequenceColour(s));\r
+ gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getWidth(),\r
+ charHeight);\r
+ gg.setColor(Color.black);\r
+ }\r
\r
- String string = s.getName();\r
- if(av.getShowFullId())\r
- string = s.getDisplayId();\r
+ if (av.rightAlignIds)\r
+ {\r
+ xPos = panelWidth - fm.stringWidth(\r
+ s.getDisplayId(av.getShowJVSuffix())\r
+ ) - 4;\r
+ }\r
\r
- gg.drawString(string,0,AlignmentUtil.getPixelHeight(starty,i,charHeight) + ypos + charHeight- (charHeight/5));\r
+ gg.drawString(s.getDisplayId(av.getShowJVSuffix()),\r
+ xPos,\r
+ ( ( (i - starty + 1) * charHeight) + ypos) - (charHeight / 5));\r
+\r
+ if (av.hasHiddenRows && av.showHiddenMarkers)\r
+ {\r
+ drawMarker(i, starty, ypos);\r
+ }\r
\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param vertical DOCUMENT ME!\r
+ */\r
public void fastPaint(int vertical)\r
{\r
- if(gg==null)\r
- { repaint(); return;}\r
+ if (gg == null)\r
+ {\r
+ repaint();\r
\r
- gg.copyArea( 0,0, getWidth(), imgHeight, 0, -vertical*av.charHeight );\r
+ return;\r
+ }\r
\r
- int ss=av.startSeq, es=av.endSeq, transY = 0;\r
- if (vertical > 0) // scroll down\r
- {\r
- ss = es - vertical;\r
- if(ss<av.startSeq) // ie scrolling too fast, more than a page at a time\r
- ss = av.startSeq;\r
- else\r
- transY = imgHeight - vertical * av.charHeight;\r
- }\r
- else if (vertical < 0)\r
- {\r
- es = ss - vertical;\r
- if(es > av.endSeq)\r
- es = av.endSeq;\r
- }\r
+ gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);\r
+\r
+ int ss = av.startSeq;\r
+ int es = av.endSeq;\r
+ int transY = 0;\r
\r
+ if (vertical > 0) // scroll down\r
+ {\r
+ ss = es - vertical;\r
\r
+ if (ss < av.startSeq)\r
+ { // ie scrolling too fast, more than a page at a time\r
+ ss = av.startSeq;\r
+ }\r
+ else\r
+ {\r
+ transY = imgHeight - (vertical * av.charHeight);\r
+ }\r
+ }\r
+ else if (vertical < 0)\r
+ {\r
+ es = ss - vertical;\r
\r
- gg.translate(0, transY);\r
+ if (es > av.endSeq)\r
+ {\r
+ es = av.endSeq;\r
+ }\r
+ }\r
\r
- drawIds(ss, es);\r
+ gg.translate(0, transY);\r
\r
- gg.translate( 0, -transY );\r
+ drawIds(ss, es);\r
\r
+ gg.translate(0, -transY);\r
\r
- fastPaint = true;\r
- repaint();\r
+ fastPaint = true;\r
+ repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\r
public void paintComponent(Graphics g)\r
{\r
g.setColor(Color.white);\r
{\r
fastPaint = false;\r
g.drawImage(image, 0, 0, this);\r
+\r
return;\r
}\r
\r
+ int oldHeight = imgHeight;\r
+\r
imgHeight = getHeight();\r
- imgHeight -= imgHeight % av.charHeight;\r
+ imgHeight -= (imgHeight % av.charHeight);\r
\r
- if (imgHeight<1)\r
+ if (imgHeight < 1)\r
+ {\r
return;\r
+ }\r
+\r
+ if (oldHeight != imgHeight || image.getWidth(this) != getWidth())\r
+ {\r
+ image = new BufferedImage(getWidth(), imgHeight,\r
+ BufferedImage.TYPE_INT_RGB);\r
+ }\r
\r
- image = new BufferedImage(getWidth(), imgHeight, BufferedImage.TYPE_INT_RGB);\r
gg = (Graphics2D) image.getGraphics();\r
+\r
//Fill in the background\r
gg.setColor(Color.white);\r
gg.fillRect(0, 0, getWidth(), imgHeight);\r
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
- av.getFont().getSize());\r
- gg.setFont(italic);\r
\r
- drawIds( av.getStartSeq(), av.endSeq);\r
+ drawIds(av.getStartSeq(), av.endSeq);\r
\r
g.drawImage(image, 0, 0, this);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param starty DOCUMENT ME!\r
+ * @param endy DOCUMENT ME!\r
+ */\r
void drawIds(int starty, int endy)\r
{\r
- Color currentColor = Color.white;\r
+ if (av.seqNameItalics)\r
+ {\r
+ idfont = new Font(av.getFont().getName(), Font.ITALIC,\r
+ av.getFont().getSize());\r
+ }\r
+ else\r
+ {\r
+ idfont = av.getFont();\r
+ }\r
+\r
+ gg.setFont(idfont);\r
+ fm = gg.getFontMetrics();\r
+\r
+ if (av.antiAlias)\r
+ {\r
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
+ }\r
+\r
+ Color currentColor = Color.white;\r
Color currentTextColor = Color.black;\r
\r
if (av.getWrapAlignment())\r
{\r
+ int maxwidth = av.alignment.getWidth();\r
+ int alheight = av.alignment.getHeight();\r
+\r
+ if (av.hasHiddenColumns)\r
+ {\r
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;\r
+ }\r
+\r
+ int annotationHeight = 0;\r
+\r
+ if (av.showAnnotation)\r
+ {\r
+ if (ap == null)\r
+ {\r
+ ap = new AnnotationPanel(av);\r
+ }\r
+\r
+ annotationHeight = ap.adjustPanelHeight();\r
+ if (labels == null)\r
+ {\r
+ labels = new AnnotationLabels(av);\r
+ }\r
+ }\r
\r
- int rowSize = av.getEndRes() - av.getStartRes();\r
- // Draw the rest of the panels\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ {\r
+ hgap += av.charHeight;\r
+ }\r
\r
- for(int ypos=2*av.charHeight, row=av.startRes;\r
- ypos <= getHeight() && row<av.alignment.getWidth();\r
- ypos += av.chunkHeight, row+=rowSize )\r
+ int cHeight = alheight * av.charHeight\r
+ + hgap\r
+ + annotationHeight;\r
+\r
+ int rowSize = av.getEndRes() - av.getStartRes();\r
+\r
+ // Draw the rest of the panels\r
+ for (int ypos = hgap, row = av.startRes;\r
+ (ypos <= getHeight()) && (row < maxwidth);\r
+ ypos += cHeight, row += rowSize)\r
+ {\r
+ for (int i = starty; i < alheight; i++)\r
+ {\r
+ SequenceI s = av.alignment.getSequenceAt(i);\r
+ if (av.hasHiddenRows)\r
{\r
- for (int i = starty; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceI s = av.alignment.getSequenceAt(i);\r
- drawIdString(gg, s, i, 0, ypos);\r
- }\r
+ setHiddenFont(s);\r
+ }\r
+ else\r
+ {\r
+ gg.setFont(idfont);\r
}\r
\r
+ drawIdString(gg, s, i, 0, ypos);\r
+ }\r
\r
- } else\r
+ if (labels != null && av.showAnnotation)\r
+ {\r
+ gg.translate(0, ypos + (alheight * av.charHeight));\r
+ labels.drawComponent(gg, getWidth());\r
+ gg.translate(0, -ypos - (alheight * av.charHeight));\r
+ }\r
+ }\r
+ }\r
+ else\r
{\r
+ //No need to hang on to labels if we're not wrapped\r
+ labels = null;\r
+\r
+ //Now draw the id strings\r
+ int panelWidth = getWidth();\r
+ int xPos = 0;\r
\r
+ SequenceI sequence;\r
//Now draw the id strings\r
for (int i = starty; i < endy; i++)\r
{\r
- // Selected sequence colours\r
+ sequence = av.alignment.getSequenceAt(i);\r
+\r
+ if (sequence == null)\r
+ {\r
+ continue;\r
+ }\r
\r
- if(searchResults!=null && searchResults.contains(av.alignment.getSequenceAt(i)))\r
+ if (av.hasHiddenRows)\r
+ {\r
+ setHiddenFont(sequence);\r
+ }\r
+\r
+ // Selected sequence colours\r
+ if ( (searchResults != null) &&\r
+ searchResults.contains(sequence))\r
{\r
- gg.setColor(Color.black);\r
currentColor = Color.black;\r
currentTextColor = Color.white;\r
- }\r
- else if (av.getSelectionGroup()!= null\r
- && av.getSelectionGroup().sequences.contains(av.alignment.getSequenceAt(i)))\r
+ }\r
+ else if ( (av.getSelectionGroup() != null) &&\r
+ av.getSelectionGroup().getSequences(null).contains(\r
+ sequence))\r
{\r
currentColor = Color.lightGray;\r
currentTextColor = Color.black;\r
}\r
else\r
{\r
- currentColor = av.alignment.getSequenceAt(i).getColor();\r
+ currentColor = av.getSequenceColour(sequence);\r
currentTextColor = Color.black;\r
}\r
\r
gg.setColor(currentColor);\r
\r
- gg.fillRect(0,\r
- AlignmentUtil.getPixelHeight(starty, i, av.charHeight),\r
- getWidth(),\r
+ gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),\r
av.charHeight);\r
\r
gg.setColor(currentTextColor);\r
- String string = av.alignment.getSequenceAt(i).getName();\r
- if(av.getShowFullId())\r
- string = av.alignment.getSequenceAt(i).getDisplayId();\r
- gg.drawString(string, 0,\r
- AlignmentUtil.getPixelHeight(starty, i, av.charHeight) +\r
- av.charHeight - (av.charHeight / 5));\r
+\r
+ String string = sequence.getDisplayId(av.getShowJVSuffix());\r
+\r
+ if (av.rightAlignIds)\r
+ {\r
+ xPos = panelWidth - fm.stringWidth(string) - 4;\r
+ }\r
+\r
+ gg.drawString(string, xPos,\r
+ ( ( (i - starty) * av.charHeight) + av.charHeight) -\r
+ (av.charHeight / 5));\r
+\r
+ if (av.hasHiddenRows && av.showHiddenMarkers)\r
+ {\r
+ drawMarker(i, starty, 0);\r
+ }\r
+\r
}\r
\r
- // add a border\r
- gg.setColor(Color.white);\r
- gg.fillRect(getWidth()-4,0,4,getHeight());\r
+ }\r
+ }\r
+\r
+ void drawMarker(int i, int starty, int yoffset)\r
+ {\r
+\r
+ SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;\r
+ //Use this method here instead of calling hiddenSeq adjust\r
+ //3 times.\r
+ int hSize = hseqs.length;\r
+\r
+ int hiddenIndex = i;\r
+ int lastIndex = i - 1;\r
+ int nextIndex = i + 1;\r
+\r
+ for (int j = 0; j < hSize; j++)\r
+ {\r
+ if (hseqs[j] != null)\r
+ {\r
+ if (j - 1 < hiddenIndex)\r
+ {\r
+ hiddenIndex++;\r
+ }\r
+ if (j - 1 < lastIndex)\r
+ {\r
+ lastIndex++;\r
+ }\r
+ if (j - 1 < nextIndex)\r
+ {\r
+ nextIndex++;\r
+ }\r
+ }\r
}\r
\r
+ boolean below = (hiddenIndex > lastIndex + 1);\r
+ boolean above = (nextIndex > hiddenIndex + 1);\r
+\r
+ gg.setColor(Color.blue);\r
+ if (below)\r
+ {\r
+ gg.fillPolygon(new int[]\r
+ {getWidth() - av.charHeight,\r
+ getWidth() - av.charHeight,\r
+ getWidth()},\r
+ new int[]\r
+ {\r
+ (i - starty) * av.charHeight + yoffset,\r
+ (i - starty) * av.charHeight + yoffset + av.charHeight / 4,\r
+ (i - starty) * av.charHeight + yoffset\r
+ }, 3);\r
+ }\r
+ if (above)\r
+ {\r
+ gg.fillPolygon(new int[]\r
+ {getWidth() - av.charHeight,\r
+ getWidth() - av.charHeight,\r
+ getWidth()},\r
+ new int[]\r
+ {\r
+ (i - starty + 1) * av.charHeight + yoffset,\r
+ (i - starty + 1) * av.charHeight + yoffset -\r
+ av.charHeight / 4,\r
+ (i - starty + 1) * av.charHeight + yoffset\r
+ }, 3);\r
+\r
+ }\r
+ }\r
+\r
+ void setHiddenFont(SequenceI seq)\r
+ {\r
+ Font bold = new Font(av.getFont().getName(), Font.BOLD,\r
+ av.getFont().getSize());\r
+\r
+ if (av.hiddenRepSequences != null &&\r
+ av.hiddenRepSequences.containsKey(seq))\r
+ {\r
+ gg.setFont(bold);\r
+ }\r
+ else\r
+ {\r
+ gg.setFont(idfont);\r
+ }\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param found DOCUMENT ME!\r
+ */\r
public void setHighlighted(java.util.Vector found)\r
{\r
searchResults = found;\r
git://source.jalview.org / jalview.git / blobdiff