-/*\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
-\r
-package jalview.appletgui;\r
-\r
-import java.awt.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\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
- boolean forOverview = false;\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 prepare(Graphics g, boolean renderGaps)\r
- {\r
- graphics = g;\r
- fm = g.getFontMetrics();\r
-\r
- this.renderGaps = renderGaps;\r
- }\r
-\r
- public Color getResidueBoxColour(SequenceI seq, int i)\r
- {\r
- allGroups = av.alignment.findAllGroups(seq);\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.globalColourScheme, seq, i);\r
- }\r
-\r
- return resBoxColour;\r
- }\r
-\r
- void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
- {\r
- if (cs != null)\r
- {\r
- resBoxColour = cs.findColour(seq.getCharAt(i), i);\r
- }\r
- else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))\r
- {\r
- resBoxColour = Color.lightGray;\r
- }\r
- else\r
- {\r
- resBoxColour = Color.white;\r
- }\r
-\r
- }\r
-\r
- public Color findSequenceColour(SequenceI seq, int i)\r
- {\r
- allGroups = av.alignment.findAllGroups(seq);\r
- drawBoxes(seq, i, i, 0);\r
- return resBoxColour;\r
- }\r
-\r
- public void drawSequence(SequenceI seq, SequenceGroup[] sg,\r
- int start, int end, int y1)\r
- {\r
- if (seq == null)\r
- {\r
- return;\r
- }\r
-\r
- allGroups = sg;\r
-\r
- drawBoxes(seq, start, end, y1);\r
-\r
- if (av.validCharWidth)\r
- {\r
- drawText(seq, start, end, y1);\r
- }\r
- }\r
-\r
- public void drawBoxes(SequenceI seq, int start, int end, int y1)\r
- {\r
- int i = start;\r
- int length = seq.getLength();\r
-\r
- int curStart = -1;\r
- int curWidth = av.charWidth;\r
-\r
- Color tempColour = null;\r
- while (i <= end)\r
- {\r
- resBoxColour = Color.white;\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
- if (resBoxColour != tempColour)\r
- {\r
- if (tempColour != null)\r
- {\r
- graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,\r
- av.charHeight);\r
- }\r
- graphics.setColor(resBoxColour);\r
-\r
- curStart = i;\r
- curWidth = av.charWidth;\r
- tempColour = resBoxColour;\r
-\r
- }\r
- else\r
- {\r
- curWidth += av.charWidth;\r
- }\r
-\r
- i++;\r
- }\r
-\r
- graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,\r
- av.charHeight);\r
- }\r
-\r
- public void drawText(SequenceI seq, int start, int end, int y1)\r
- {\r
- Font boldFont = null;\r
- boolean bold = false;\r
- if (av.upperCasebold)\r
- {\r
- boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);\r
-\r
- graphics.setFont(av.getFont());\r
- }\r
-\r
- y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady\r
-\r
- int charOffset = 0;\r
-\r
- // Need to find the sequence position here.\r
- if (end + 1 >= seq.getLength())\r
- {\r
- end = seq.getLength() - 1;\r
- }\r
-\r
- char s = ' ';\r
-\r
- for (int i = start; i <= end; i++)\r
- {\r
- graphics.setColor(Color.black);\r
-\r
- s = seq.getCharAt(i);\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
- if (av.getShowBoxes())\r
- {\r
- graphics.setColor(resBoxColour.darker());\r
- }\r
- else\r
- {\r
- graphics.setColor(resBoxColour);\r
- }\r
- }\r
- }\r
-\r
- if (av.upperCasebold)\r
- {\r
- fm = graphics.getFontMetrics();\r
- if ('A' <= s && s <= 'Z')\r
- {\r
- if (!bold)\r
- {\r
-\r
- graphics.setFont(boldFont);\r
- }\r
- bold = true;\r
- }\r
- else if (bold)\r
- {\r
- graphics.setFont(av.font);\r
- bold = false;\r
- }\r
-\r
- }\r
-\r
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
- graphics.drawString(String.valueOf(s),\r
- charOffset + av.charWidth * (i - start),\r
- y1);\r
- }\r
-\r
- }\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 && allGroups[i].getEndRes() >= res)\r
- {\r
- currentSequenceGroup = allGroups[i];\r
- return true;\r
- }\r
- }\r
-\r
- return false;\r
- }\r
-\r
- public void drawHighlightedText(SequenceI seq, int start, int end, int x1,\r
- int y1)\r
- {\r
- int pady = av.charHeight / 5;\r
- int charOffset = 0;\r
- graphics.setColor(Color.black);\r
- graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);\r
- graphics.setColor(Color.white);\r
-\r
- char s = '~';\r
- // Need to find the sequence position here.\r
- if (av.validCharWidth)\r
- {\r
- for (int i = start; i <= end; i++)\r
- {\r
- if (i < seq.getLength())\r
- {\r
- s = seq.getCharAt(i);\r
- }\r
-\r
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
- graphics.drawString(String.valueOf(s),\r
- charOffset + x1 + av.charWidth * (i - start),\r
- y1 + av.charHeight - pady);\r
- }\r
- }\r
- }\r
-\r
- public void drawCursor(SequenceI seq, int res, int x1, int y1)\r
- {\r
- int pady = av.charHeight / 5;\r
- int charOffset = 0;\r
- graphics.setColor(Color.black);\r
- graphics.fillRect(x1, y1, av.charWidth, av.charHeight);\r
- graphics.setColor(Color.white);\r
-\r
- graphics.setColor(Color.white);\r
-\r
- char s = seq.getCharAt(res);\r
- if (av.validCharWidth)\r
- {\r
-\r
- charOffset = (av.charWidth - fm.charWidth(s)) / 2;\r
- graphics.drawString(String.valueOf(s),\r
- charOffset + x1,\r
- (y1 + av.charHeight) - pady);\r
- }\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+import jalview.schemes.*;
+
+public class SequenceRenderer implements jalview.api.SequenceRenderer
+{
+ AlignViewport av;
+
+ FontMetrics fm;
+
+ boolean renderGaps = true;
+
+ SequenceGroup currentSequenceGroup = null;
+
+ SequenceGroup[] allGroups = null;
+
+ Color resBoxColour;
+
+ Graphics graphics;
+
+ boolean forOverview = false;
+
+ 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();
+
+ 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;
+ }
+
+ void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+ {
+ if (cs != null)
+ {
+ resBoxColour = cs.findColour(seq.getCharAt(i), i);
+ }
+ else if (forOverview
+ && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+ {
+ resBoxColour = Color.lightGray;
+ }
+ else
+ {
+ resBoxColour = Color.white;
+ }
+
+ }
+
+ public Color findSequenceColour(SequenceI seq, int i)
+ {
+ allGroups = av.alignment.findAllGroups(seq);
+ drawBoxes(seq, i, i, 0);
+ return resBoxColour;
+ }
+
+ public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,
+ int end, int y1)
+ {
+ if (seq == null)
+ {
+ return;
+ }
+
+ allGroups = sg;
+
+ drawBoxes(seq, start, end, y1);
+
+ if (av.validCharWidth)
+ {
+ drawText(seq, start, end, y1);
+ }
+ }
+
+ public 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.getGlobalColourScheme(), 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);
+ }
+
+ public void drawText(SequenceI seq, int start, int end, int y1)
+ {
+ Font boldFont = null;
+ boolean bold = false;
+ if (av.upperCasebold)
+ {
+ boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
+
+ graphics.setFont(av.getFont());
+ }
+
+ y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
+
+ int charOffset = 0;
+
+ // Need to find the sequence position here.
+ if (end + 1 >= seq.getLength())
+ {
+ end = seq.getLength() - 1;
+ }
+
+ char s = ' ';
+
+ 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());
+ }
+ if (currentSequenceGroup.getShowNonconserved())
+ {
+ // cheat - use this if we have a consensus for each group: s =
+ // getDisplayChar(currentSequenceGroup.getConsensus(), i, s, '.');
+ s = getDisplayChar(av.consensus, i, s, '.');
+ }
+ }
+ else
+ {
+ if (!av.getShowText())
+ {
+ continue;
+ }
+
+ if (av.getColourText())
+ {
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
+ if (av.getShowBoxes())
+ {
+ graphics.setColor(resBoxColour.darker());
+ }
+ else
+ {
+ graphics.setColor(resBoxColour);
+ }
+ }
+ if (av.getShowunconserved())
+ {
+ s = getDisplayChar(av.consensus, i, s, '.');
+
+ }
+ }
+
+ if (av.upperCasebold)
+ {
+ fm = graphics.getFontMetrics();
+ if ('A' <= s && s <= 'Z')
+ {
+ if (!bold)
+ {
+
+ graphics.setFont(boldFont);
+ }
+ bold = true;
+ }
+ else if (bold)
+ {
+ graphics.setFont(av.font);
+ bold = false;
+ }
+
+ }
+
+ charOffset = (av.charWidth - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s), charOffset + av.charWidth
+ * (i - start), y1);
+ }
+
+ }
+
+ private char getDisplayChar(AlignmentAnnotation consensus, int position,
+ char s, char c)
+ {
+ char conschar = consensus.annotations[position].displayCharacter
+ .charAt(0);
+ if (conschar != '-' && s == conschar)
+ {
+ s = c;
+ }
+ return s;
+ }
+
+ 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;
+ }
+
+ 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.getCharAt(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);
+ graphics.setColor(Color.white);
+
+ graphics.setColor(Color.white);
+
+ char s = seq.getCharAt(res);
+ if (av.validCharWidth)
+ {
+
+ 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