-/*\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 jalview.schemes.*;\r
-\r
-import java.awt.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class SequenceRenderer\r
-{\r
- AlignViewport av;\r
- FontMetrics fm;\r
- boolean renderGaps = true;\r
- SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup[] allGroups = null;\r
- Color resBoxColour;\r
- Graphics graphics;\r
-\r
- /**\r
- * Creates a new SequenceRenderer object.\r
- *\r
- * @param av DOCUMENT ME!\r
- */\r
- public SequenceRenderer(AlignViewport av)\r
- {\r
- this.av = av;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param b DOCUMENT ME!\r
- */\r
- public void renderGaps(boolean b)\r
- {\r
- renderGaps = b;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param cs DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- * @param i DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
- {\r
- getBoxColour(cs, seq, i);\r
-\r
- return resBoxColour;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param cs DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- * @param i DOCUMENT ME!\r
- */\r
- void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
- {\r
- if (cs != null)\r
- {\r
- resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);\r
- }\r
- else\r
- {\r
- resBoxColour = Color.white;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- * @param sg DOCUMENT ME!\r
- * @param start DOCUMENT ME!\r
- * @param end DOCUMENT ME!\r
- * @param x1 DOCUMENT ME!\r
- * @param y1 DOCUMENT ME!\r
- * @param width DOCUMENT ME!\r
- * @param height DOCUMENT ME!\r
- */\r
- public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
- int start, int end, int x1, int y1, int width, int height)\r
- {\r
- allGroups = sg;\r
-\r
- graphics = g;\r
-\r
- drawBoxes(seq, start, end, x1, y1, width, height);\r
-\r
- fm = g.getFontMetrics();\r
- drawText(seq, start, end, x1, y1, width, height);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param seq DOCUMENT ME!\r
- * @param start DOCUMENT ME!\r
- * @param end DOCUMENT ME!\r
- * @param x1 DOCUMENT ME!\r
- * @param y1 DOCUMENT ME!\r
- * @param width DOCUMENT ME!\r
- * @param height DOCUMENT ME!\r
- */\r
- public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,\r
- int width, int height)\r
- {\r
- int i = start;\r
- int length = seq.getLength();\r
-\r
- int curStart = -1;\r
- int curWidth = width;\r
-\r
- Color tempColour = null;\r
-\r
- while (i <= end)\r
- {\r
- resBoxColour = Color.white;\r
-\r
- if (i < length)\r
- {\r
- if (inCurrentSequenceGroup(i))\r
- {\r
- if (currentSequenceGroup.getDisplayBoxes())\r
- {\r
- getBoxColour(currentSequenceGroup.cs, seq, i);\r
- }\r
- }\r
- else if (av.getShowBoxes())\r
- {\r
- getBoxColour(av.getGlobalColourScheme(), seq, i);\r
- }\r
-\r
- }\r
-\r
- if (resBoxColour != tempColour)\r
- {\r
- if (tempColour != null)\r
- {\r
- graphics.fillRect(x1 + (width * (curStart - start)), y1,\r
- curWidth, height);\r
- }\r
-\r
- graphics.setColor(resBoxColour);\r
-\r
- curStart = i;\r
- curWidth = width;\r
- tempColour = resBoxColour;\r
- }\r
- else\r
- {\r
- curWidth += width;\r
- }\r
-\r
- i++;\r
- }\r
-\r
- graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,\r
- height);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param seq DOCUMENT ME!\r
- * @param start DOCUMENT ME!\r
- * @param end DOCUMENT ME!\r
- * @param x1 DOCUMENT ME!\r
- * @param y1 DOCUMENT ME!\r
- * @param width DOCUMENT ME!\r
- * @param height DOCUMENT ME!\r
- */\r
- public void drawText(SequenceI seq, int start, int end, int x1, int y1,\r
- int width, int height)\r
- {\r
- int pady = height / 5;\r
- int charOffset = 0;\r
- char s;\r
-\r
- // Need to find the sequence position here.\r
- String sequence = seq.getSequence();\r
-\r
- if(end+1>=seq.getLength())\r
- end = seq.getLength()-1;\r
-\r
- for (int i = start; i <= end; i++)\r
- {\r
- graphics.setColor(Color.black);\r
-\r
- s = sequence.charAt(i);\r
-\r
- if (!renderGaps && jalview.util.Comparison.isGap(s))\r
- {\r
- continue;\r
- }\r
-\r
- if (inCurrentSequenceGroup(i))\r
- {\r
- if (!currentSequenceGroup.getDisplayText())\r
- {\r
- continue;\r
- }\r
-\r
- if (currentSequenceGroup.getColourText())\r
- {\r
- getBoxColour(currentSequenceGroup.cs, seq, i);\r
- graphics.setColor(resBoxColour.darker());\r
- }\r
- }\r
- else\r
- {\r
- if (!av.getShowText())\r
- {\r
- continue;\r
- }\r
-\r
- if (av.getColourText())\r
- {\r
- getBoxColour(av.getGlobalColourScheme(), seq, i);\r
-\r
- if (av.getShowBoxes())\r
- {\r
- graphics.setColor(resBoxColour.darker());\r
- }\r
- else\r
- {\r
- graphics.setColor(resBoxColour);\r
- }\r
- }\r
- }\r
-\r
- charOffset = (width - fm.charWidth(s)) / 2;\r
- graphics.drawString(String.valueOf(s),\r
- charOffset + x1 + (int)(width * (i - start)), (y1 + height) - pady);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param res DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- boolean inCurrentSequenceGroup(int res)\r
- {\r
- if (allGroups == null)\r
- {\r
- return false;\r
- }\r
-\r
- for (int i = 0; i < allGroups.length; i++)\r
- {\r
- if ((allGroups[i].getStartRes() <= res) &&\r
- (allGroups[i].getEndRes() >= res))\r
- {\r
- currentSequenceGroup = allGroups[i];\r
-\r
- return true;\r
- }\r
- }\r
-\r
- return false;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param seq DOCUMENT ME!\r
- * @param start DOCUMENT ME!\r
- * @param end DOCUMENT ME!\r
- * @param x1 DOCUMENT ME!\r
- * @param y1 DOCUMENT ME!\r
- * @param width DOCUMENT ME!\r
- * @param height DOCUMENT ME!\r
- */\r
- public void drawHighlightedText(SequenceI seq, int start, int end, int x1,\r
- int y1, int width, int height)\r
- {\r
- int pady = height / 5;\r
- int charOffset = 0;\r
- graphics.setColor(Color.BLACK);\r
- graphics.fillRect(x1, y1, width * (end - start + 1), height);\r
- graphics.setColor(Color.white);\r
-\r
- char s = '~';\r
-\r
- // Need to find the sequence position here.\r
- for (int i = start; i <= end; i++)\r
- {\r
- if (i < seq.getLength())\r
- {\r
- s = seq.getSequence().charAt(i);\r
- }\r
-\r
- charOffset = (width - fm.charWidth(s)) / 2;\r
- graphics.drawString(String.valueOf(s),\r
- charOffset + x1 + (width * (i - start)), (y1 + height) - pady);\r
- }\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 jalview.schemes.*;
+
+import java.awt.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceRenderer
+{
+ AlignViewport av;
+ FontMetrics fm;
+ boolean renderGaps = true;
+ SequenceGroup currentSequenceGroup = null;
+ SequenceGroup[] allGroups = null;
+ Color resBoxColour;
+ Graphics graphics;
+ boolean monospacedFont;
+ boolean forOverview = false;
+
+ /**
+ * Creates a new SequenceRenderer object.
+ *
+ * @param av DOCUMENT ME!
+ */
+ public SequenceRenderer(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void prepare(Graphics g, boolean renderGaps)
+ {
+ graphics = g;
+ fm = g.getFontMetrics();
+
+ // If EPS graphics, stringWidth will be a double, not an int
+ double dwidth = fm.getStringBounds("M", g).getWidth();
+
+ monospacedFont =
+ (dwidth == fm.getStringBounds("|",g).getWidth()
+ && (float)av.charWidth == dwidth);
+
+ this.renderGaps = renderGaps;
+ }
+
+
+ public Color getResidueBoxColour(SequenceI seq, int i)
+ {
+ allGroups = av.alignment.findAllGroups(seq);
+
+ if (inCurrentSequenceGroup(i))
+ {
+ if (currentSequenceGroup.getDisplayBoxes())
+ {
+ getBoxColour(currentSequenceGroup.cs, seq, i);
+ }
+ }
+ else if (av.getShowBoxes())
+ {
+ getBoxColour(av.globalColourScheme, seq, i);
+ }
+
+ return resBoxColour;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cs DOCUMENT ME!
+ * @param seq DOCUMENT ME!
+ * @param i DOCUMENT ME!
+ */
+ void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+ {
+ if (cs != null)
+ {
+ resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
+ }
+ else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+ {
+ resBoxColour = Color.lightGray;
+ }
+ else
+ {
+ resBoxColour = Color.white;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g DOCUMENT ME!
+ * @param seq DOCUMENT ME!
+ * @param sg DOCUMENT ME!
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ * @param x1 DOCUMENT ME!
+ * @param y1 DOCUMENT ME!
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ */
+ public void drawSequence(SequenceI seq, SequenceGroup[] sg,
+ int start, int end, int y1)
+ {
+ allGroups = sg;
+
+ drawBoxes(seq, start, end, y1);
+
+ if (av.validCharWidth)
+ drawText(seq, start, end, y1);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq DOCUMENT ME!
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ * @param x1 DOCUMENT ME!
+ * @param y1 DOCUMENT ME!
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ */
+ public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)
+ {
+ int i = start;
+ int length = seq.getLength();
+
+ int curStart = -1;
+ int curWidth = av.charWidth;
+
+ Color tempColour = null;
+
+ while (i <= end)
+ {
+ resBoxColour = Color.white;
+
+ if (i < length)
+ {
+ if (inCurrentSequenceGroup(i))
+ {
+ if (currentSequenceGroup.getDisplayBoxes())
+ {
+ getBoxColour(currentSequenceGroup.cs, seq, i);
+ }
+ }
+ else if (av.getShowBoxes())
+ {
+ getBoxColour(av.globalColourScheme, seq, i);
+ }
+
+ }
+
+ if (resBoxColour != tempColour)
+ {
+ if (tempColour != null)
+ {
+ graphics.fillRect( av.charWidth * (curStart - start), y1,
+ curWidth, av.charHeight);
+ }
+
+ graphics.setColor(resBoxColour);
+
+ curStart = i;
+ curWidth = av.charWidth;
+ tempColour = resBoxColour;
+ }
+ else
+ {
+ curWidth += av.charWidth;
+ }
+
+ i++;
+ }
+
+ graphics.fillRect( av.charWidth * (curStart - start), y1, curWidth,
+ av.charHeight);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq DOCUMENT ME!
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ * @param x1 DOCUMENT ME!
+ * @param y1 DOCUMENT ME!
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ */
+ public void drawText(SequenceI seq, int start, int end, int y1)
+ {
+ y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+ int charOffset = 0;
+ char s;
+
+ if(end+1>=seq.getLength())
+ end = seq.getLength()-1;
+ graphics.setColor(Color.black);
+
+
+ if(monospacedFont && av.showText && allGroups.length==0 && !av.getColourText())
+ {
+ if(av.renderGaps)
+ graphics.drawString(seq.getSequence(start, end + 1), 0, y1);
+ else
+ {
+ char gap = av.getGapCharacter();
+ graphics.drawString( seq.getSequence(start, end+1).replace(gap, ' '), 0, y1);
+ }
+ }
+ else
+ {
+ for (int i = start; i <= end; i++)
+ {
+ graphics.setColor(Color.black);
+ s = seq.getCharAt(i);
+ if (!renderGaps && jalview.util.Comparison.isGap(s))
+ {
+ continue;
+ }
+
+ if (inCurrentSequenceGroup(i))
+ {
+ if (!currentSequenceGroup.getDisplayText())
+ {
+ continue;
+ }
+
+ if (currentSequenceGroup.getColourText())
+ {
+ getBoxColour(currentSequenceGroup.cs, seq, i);
+ graphics.setColor(resBoxColour.darker());
+ }
+ }
+ else
+ {
+ if (!av.getShowText())
+ {
+ continue;
+ }
+
+ if (av.getColourText())
+ {
+ getBoxColour(av.globalColourScheme, seq, i);
+
+ if (av.getShowBoxes())
+ {
+ graphics.setColor(resBoxColour.darker());
+ }
+ else
+ {
+ graphics.setColor(resBoxColour);
+ }
+ }
+ }
+
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+
+ // System.out.print(s);
+ graphics.drawString(String.valueOf(s),
+ charOffset + av.charWidth * (i - start),
+ y1);
+
+ }
+ // System.out.println("\n");
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param res DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ boolean inCurrentSequenceGroup(int res)
+ {
+ if (allGroups == null)
+ {
+ return false;
+ }
+
+ for (int i = 0; i < allGroups.length; i++)
+ {
+ if ((allGroups[i].getStartRes() <= res) &&
+ (allGroups[i].getEndRes() >= res))
+ {
+ currentSequenceGroup = allGroups[i];
+
+ return true;
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq DOCUMENT ME!
+ * @param start DOCUMENT ME!
+ * @param end DOCUMENT ME!
+ * @param x1 DOCUMENT ME!
+ * @param y1 DOCUMENT ME!
+ * @param width DOCUMENT ME!
+ * @param height DOCUMENT ME!
+ */
+ public void drawHighlightedText(SequenceI seq, int start, int end, int x1, int y1)
+ {
+ int pady = av.charHeight / 5;
+ int charOffset = 0;
+ graphics.setColor(Color.BLACK);
+ graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
+ graphics.setColor(Color.white);
+
+ char s = '~';
+
+ // Need to find the sequence position here.
+ if(av.validCharWidth)
+ {
+ for (int i = start; i <= end; i++)
+ {
+ if (i < seq.getLength())
+ {
+ s = seq.getSequence().charAt(i);
+ }
+
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s),
+ charOffset + x1 + (av.charWidth * (i - start)),
+ (y1 + av.charHeight) - pady);
+ }
+ }
+ }
+
+ public void drawCursor(SequenceI seq, int res, int x1, int y1)
+ {
+ int pady = av.charHeight / 5;
+ int charOffset = 0;
+ graphics.setColor(Color.black);
+ graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
+
+ if(av.validCharWidth)
+ {
+ graphics.setColor(Color.white);
+
+ char s = seq.getCharAt(res);
+
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s),
+ charOffset + x1,
+ (y1 + av.charHeight) - pady);
+ }
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff