-/*\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
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import java.awt.*;\r
-import java.awt.image.*;\r
-\r
-import javax.swing.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class IdCanvas extends JPanel\r
-{\r
- protected AlignViewport av;\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
- boolean fastPaint = false;\r
- java.util.Vector searchResults;\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, av.alignment);\r
- }\r
-\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 charHeight = av.charHeight;\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().sequences.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(s.getColor());\r
- gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),\r
- charHeight);\r
- gg.setColor(Color.black);\r
- }\r
-\r
-\r
- gg.drawString( s.getDisplayId(av.getShowJVSuffix()),\r
- 0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));\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
- {\r
- repaint();\r
-\r
- return;\r
- }\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
- if (es > av.endSeq)\r
- {\r
- es = av.endSeq;\r
- }\r
- }\r
-\r
- gg.translate(0, transY);\r
-\r
- drawIds(ss, es);\r
-\r
- gg.translate(0, -transY);\r
-\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
- g.fillRect(0, 0, getWidth(), getHeight());\r
-\r
- if (fastPaint)\r
- {\r
- fastPaint = false;\r
- g.drawImage(image, 0, 0, this);\r
-\r
- return;\r
- }\r
-\r
- imgHeight = getHeight();\r
- imgHeight -= (imgHeight % av.charHeight);\r
-\r
- if (imgHeight < 1)\r
- {\r
- return;\r
- }\r
-\r
- image = new BufferedImage(getWidth(), imgHeight,\r
- 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
-\r
-\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
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
- av.getFont().getSize());\r
- gg.setFont(italic);\r
-\r
- if (av.antiAlias)\r
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
-\r
- Color currentColor = Color.white;\r
- Color currentTextColor = Color.black;\r
-\r
- if (av.getWrapAlignment())\r
- {\r
- int annotationHeight = 0;\r
- AnnotationLabels labels = null;\r
-\r
- if(av.showAnnotation)\r
- {\r
- AnnotationPanel ap = new AnnotationPanel(av);\r
- annotationHeight = ap.adjustPanelHeight();\r
- labels = new AnnotationLabels(av);\r
- }\r
-\r
- int hgap = av.charHeight;\r
- if (av.scaleAboveWrapped)\r
- hgap += av.charHeight;\r
-\r
- int cHeight = av.getAlignment().getHeight() * 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 < av.alignment.getWidth());\r
- ypos += cHeight, row += rowSize)\r
- {\r
- for (int i = starty; i < av.alignment.getHeight(); i++)\r
- {\r
-\r
- SequenceI s = av.alignment.getSequenceAt(i);\r
- gg.setFont(italic);\r
- drawIdString(gg, s, i, 0, ypos);\r
- }\r
-\r
- if(labels!=null)\r
- {\r
- gg.translate(0, ypos+(av.getAlignment().getHeight() * av.charHeight));\r
- labels.drawComponent(gg, getWidth());\r
- gg.translate(0, -ypos-(av.getAlignment().getHeight() * av.charHeight));\r
-\r
- }\r
- }\r
- }\r
- else\r
- {\r
- //Now draw the id strings\r
- int tmp, hiddenIndex = starty;\r
- boolean markHidden = false;\r
- for (int i = starty; i < endy; i++)\r
- {\r
- if (av.hasHiddenRows)\r
- {\r
- tmp = av.adjustForHiddenSeqs(i);\r
- if(hiddenIndex != tmp)\r
- {\r
- hiddenIndex = tmp;\r
- markHidden = true;\r
- }\r
- else\r
- markHidden = false;\r
-\r
- hiddenIndex++;\r
- }\r
-\r
- if(av.hasHiddenRows && av.alignment.getSequenceAt(i).getHiddenSequences()!=null)\r
- {\r
- currentTextColor = Color.blue;\r
- }\r
- else\r
- // Selected sequence colours\r
- if ((searchResults != null) &&\r
- searchResults.contains(av.alignment.getSequenceAt(i)))\r
- {\r
- currentColor = Color.black;\r
- currentTextColor = Color.white;\r
- }\r
- else if ((av.getSelectionGroup() != null) &&\r
- av.getSelectionGroup().sequences.contains(\r
- av.alignment.getSequenceAt(i)))\r
- {\r
- currentColor = Color.lightGray;\r
- currentTextColor = Color.black;\r
- }\r
- else\r
- {\r
- currentColor = av.alignment.getSequenceAt(i).getColor();\r
- currentTextColor = Color.black;\r
- }\r
-\r
- gg.setColor(currentColor);\r
-\r
- gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),\r
- av.charHeight);\r
-\r
- if (markHidden)\r
- {\r
- gg.setColor(Color.blue);\r
- // gg.drawLine(0, (i-starty)*av.charHeight, getWidth(),(i-starty)*av.charHeight);\r
- gg.fillPolygon(new int[] { getWidth() - av.charHeight,\r
- getWidth() - av.charHeight,\r
- getWidth() },\r
- new int[]\r
- {\r
- (i-starty)*av.charHeight -av.charHeight/4,\r
- (i-starty)*av.charHeight +av.charHeight/4,\r
- (i-starty)*av.charHeight\r
- }, 3);\r
-\r
- }\r
-\r
- gg.setColor(currentTextColor);\r
-\r
- String string = av.alignment.getSequenceAt(i).getDisplayId( av.getShowJVSuffix());\r
-\r
- gg.drawString(string, 0,\r
- (((i - starty) * av.charHeight) + av.charHeight) -\r
- (av.charHeight / 5));\r
- }\r
-\r
- // add a border\r
- // gg.setColor(Color.cyan);\r
- // gg.fillRect(getWidth() - 4, 0, 4, getHeight());\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
- repaint();\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import jalview.datamodel.*;
+
+import java.awt.*;
+import java.awt.image.*;
+
+import javax.swing.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdCanvas extends JPanel
+{
+ protected AlignViewport av;
+ protected boolean showScores = true;
+ protected int maxIdLength = -1;
+ protected String maxIdStr = null;
+ BufferedImage image;
+ Graphics2D gg;
+ int imgHeight = 0;
+ boolean fastPaint = false;
+ java.util.Vector searchResults;
+
+ /**
+ * Creates a new IdCanvas object.
+ *
+ * @param av DOCUMENT ME!
+ */
+ public IdCanvas(AlignViewport av)
+ {
+ setLayout(new BorderLayout());
+ this.av = av;
+ PaintRefresher.Register(this, av.alignment);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gg DOCUMENT ME!
+ * @param s DOCUMENT ME!
+ * @param i DOCUMENT ME!
+ * @param starty DOCUMENT ME!
+ * @param ypos DOCUMENT ME!
+ */
+ public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty, int ypos)
+ {
+ int charHeight = av.charHeight;
+
+ if ((searchResults != null) && searchResults.contains(s))
+ {
+ gg.setColor(Color.black);
+ gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+ charHeight);
+ gg.setColor(Color.white);
+ }
+ else if ((av.getSelectionGroup() != null) &&
+ av.getSelectionGroup().getSequences(false).contains(s))
+ {
+ gg.setColor(Color.lightGray);
+ gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+ charHeight);
+ gg.setColor(Color.white);
+ }
+ else
+ {
+ gg.setColor(s.getColor());
+ gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
+ charHeight);
+ gg.setColor(Color.black);
+ }
+
+
+ gg.drawString( s.getDisplayId(av.getShowJVSuffix()),
+ 0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
+
+ if (av.hasHiddenRows && av.showHiddenMarkers)
+ drawMarker(i, starty, ypos);
+
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param vertical DOCUMENT ME!
+ */
+ public void fastPaint(int vertical)
+ {
+ if (gg == null)
+ {
+ repaint();
+
+ return;
+ }
+
+ gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight);
+
+ int ss = av.startSeq;
+ int es = av.endSeq;
+ int transY = 0;
+
+ if (vertical > 0) // scroll down
+ {
+ ss = es - vertical;
+
+ if (ss < av.startSeq)
+ { // ie scrolling too fast, more than a page at a time
+ ss = av.startSeq;
+ }
+ else
+ {
+ transY = imgHeight - (vertical * av.charHeight);
+ }
+ }
+ else if (vertical < 0)
+ {
+ es = ss - vertical;
+
+ if (es > av.endSeq)
+ {
+ es = av.endSeq;
+ }
+ }
+
+ gg.translate(0, transY);
+
+ drawIds(ss, es);
+
+ gg.translate(0, -transY);
+
+ fastPaint = true;
+ repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ */
+ public void paintComponent(Graphics g)
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getWidth(), getHeight());
+
+ if (fastPaint)
+ {
+ fastPaint = false;
+ g.drawImage(image, 0, 0, this);
+
+ return;
+ }
+
+ int oldHeight = imgHeight;
+
+ imgHeight = getHeight();
+ imgHeight -= (imgHeight % av.charHeight);
+
+ if (imgHeight < 1)
+ {
+ return;
+ }
+
+ if(oldHeight!=imgHeight || image.getWidth(this)!=getWidth())
+ {
+ image = new BufferedImage(getWidth(), imgHeight,
+ BufferedImage.TYPE_INT_RGB);
+ }
+
+ gg = (Graphics2D) image.getGraphics();
+ //Fill in the background
+ gg.setColor(Color.white);
+ gg.fillRect(0, 0, getWidth(), imgHeight);
+
+ drawIds(av.getStartSeq(), av.endSeq);
+
+ g.drawImage(image, 0, 0, this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param starty DOCUMENT ME!
+ * @param endy DOCUMENT ME!
+ */
+ void drawIds(int starty, int endy)
+ {
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+ av.getFont().getSize());
+
+ gg.setFont(italic);
+
+ if (av.antiAlias)
+ gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+
+ Color currentColor = Color.white;
+ Color currentTextColor = Color.black;
+
+ if (av.getWrapAlignment())
+ {
+ int maxwidth = av.alignment.getWidth();
+ int alheight = av.alignment.getHeight();
+
+ if (av.hasHiddenColumns)
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+
+ int annotationHeight = 0;
+ AnnotationLabels labels = null;
+
+ if(av.showAnnotation)
+ {
+ AnnotationPanel ap = new AnnotationPanel(av);
+ annotationHeight = ap.adjustPanelHeight();
+ labels = new AnnotationLabels(av);
+ }
+
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ hgap += av.charHeight;
+
+ int cHeight = alheight * av.charHeight
+ + hgap
+ + annotationHeight;
+
+ int rowSize = av.getEndRes() - av.getStartRes();
+
+
+ // Draw the rest of the panels
+ for (int ypos = hgap, row = av.startRes;
+ (ypos <= getHeight()) && (row < maxwidth);
+ ypos += cHeight, row += rowSize)
+ {
+ for (int i = starty; i < alheight; i++)
+ {
+ if (av.hasHiddenRows)
+ {
+ setHiddenFont(i);
+ }
+ else
+ gg.setFont(italic);
+
+ SequenceI s = av.alignment.getSequenceAt(i);
+ drawIdString(gg, s, i, 0, ypos);
+ }
+
+ if(labels!=null)
+ {
+ gg.translate(0, ypos+(alheight * av.charHeight));
+ labels.drawComponent(gg, getWidth());
+ gg.translate(0, -ypos-(alheight * av.charHeight));
+ }
+
+
+ }
+ }
+ else
+ {
+ //Now draw the id strings
+
+ //Now draw the id strings
+ for (int i = starty; i < endy; i++)
+ {
+ if (av.hasHiddenRows)
+ {
+ setHiddenFont(i);
+ }
+
+ // Selected sequence colours
+ if ( (searchResults != null) &&
+ searchResults.contains(av.alignment.getSequenceAt(i)))
+ {
+ currentColor = Color.black;
+ currentTextColor = Color.white;
+ }
+ else if ( (av.getSelectionGroup() != null) &&
+ av.getSelectionGroup().getSequences(false).contains(
+ av.alignment.getSequenceAt(i)))
+ {
+ currentColor = Color.lightGray;
+ currentTextColor = Color.black;
+ }
+ else
+ {
+ currentColor = av.alignment.getSequenceAt(i).getColor();
+ currentTextColor = Color.black;
+ }
+
+ gg.setColor(currentColor);
+
+ gg.fillRect(0, (i - starty) * av.charHeight, getWidth(),
+ av.charHeight);
+
+ gg.setColor(currentTextColor);
+
+ String string = av.alignment.getSequenceAt(i).getDisplayId( av.getShowJVSuffix());
+
+ gg.drawString(string, 0,
+ (((i - starty) * av.charHeight) + av.charHeight) -
+ (av.charHeight / 5));
+
+ if(av.hasHiddenRows && av.showHiddenMarkers)
+ drawMarker(i, starty, 0);
+
+ }
+
+ }
+ }
+
+ void drawMarker(int i, int starty, int yoffset)
+ {
+ int hiddenIndex = av.adjustForHiddenSeqs(i);
+ int lastIndex = av.adjustForHiddenSeqs(i - 1);
+ int nextIndex = av.adjustForHiddenSeqs(i + 1);
+
+ boolean below = (hiddenIndex > lastIndex + 1);
+ boolean above = (nextIndex>hiddenIndex+1);
+
+ gg.setColor(Color.blue);
+ if(below)
+ {
+ gg.fillPolygon(new int[]
+ {getWidth()- av.charHeight,
+ getWidth()- av.charHeight,
+ getWidth()},
+ new int[]
+ {
+ (i - starty) * av.charHeight +yoffset,
+ (i - starty) * av.charHeight +yoffset+ av.charHeight / 4,
+ (i - starty) * av.charHeight+yoffset
+ }, 3);
+ }
+ if(above)
+ {
+ gg.fillPolygon(new int[]
+ {getWidth()- av.charHeight,
+ getWidth()- av.charHeight,
+ getWidth() },
+ new int[]
+ {
+ (i - starty+1) * av.charHeight +yoffset,
+ (i - starty+1) * av.charHeight +yoffset- av.charHeight / 4,
+ (i - starty+1) * av.charHeight +yoffset
+ }, 3);
+
+ }
+ }
+
+ void setHiddenFont(int i)
+ {
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC,
+ av.getFont().getSize());
+ Font bold = new Font(av.getFont().getName(), Font.BOLD,
+ av.getFont().getSize());
+
+ if (av.alignment.getSequenceAt(i).getHiddenSequences() != null)
+ gg.setFont(bold);
+ else
+ gg.setFont(italic);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param found DOCUMENT ME!
+ */
+ public void setHighlighted(java.util.Vector found)
+ {
+ searchResults = found;
+ repaint();
+ }
+}
git://source.jalview.org / jalview.git / blobdiff