-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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.api.FeatureRenderer;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.Comparison;
-
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Graphics;
-
-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.getAlignment().findAllGroups(seq);
-
- if (inCurrentSequenceGroup(i))
- {
- if (currentSequenceGroup.getDisplayBoxes())
- {
- getBoxColour(currentSequenceGroup.cs, seq, i);
- }
- }
- else if (av.getShowBoxes())
- {
- getBoxColour(av.getGlobalColourScheme(), seq, i);
- }
-
- return resBoxColour;
- }
-
- /**
- * Get the residue colour at the given sequence position - as determined by
- * the sequence group colour (if any), else the colour scheme, possibly
- * overridden by a feature colour.
- *
- * @param seq
- * @param position
- * @param fr
- * @return
- */
- @Override
- public Color getResidueColour(final SequenceI seq, int position,
- FeatureRenderer fr)
- {
- // TODO replace 8 or so code duplications with calls to this method
- // (refactored as needed)
- Color col = getResidueBoxColour(seq, position);
-
- if (fr != null)
- {
- col = fr.findFeatureColour(col, seq, position);
- }
- return col;
- }
-
- void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
- {
- if (cs != null)
- {
- resBoxColour = cs.findColour(seq.getCharAt(i), i, seq);
- }
- else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
- {
- resBoxColour = Color.lightGray;
- }
- else
- {
- resBoxColour = Color.white;
- }
-
- }
-
- public Color findSequenceColour(SequenceI seq, int i)
- {
- allGroups = av.getAlignment().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.getCharWidth(), avCharWidth = av.getCharWidth(), avCharHeight = av
- .getCharHeight();
-
- 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(avCharWidth * (curStart - start), y1, curWidth,
- avCharHeight);
- }
- graphics.setColor(resBoxColour);
-
- curStart = i;
- curWidth = avCharWidth;
- tempColour = resBoxColour;
-
- }
- else
- {
- curWidth += avCharWidth;
- }
-
- i++;
- }
-
- graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,
- avCharHeight);
- }
-
- public void drawText(SequenceI seq, int start, int end, int y1)
- {
- int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
- Font boldFont = null;
- boolean bold = false;
- if (av.isUpperCasebold())
- {
- boldFont = new Font(av.getFont().getName(), Font.BOLD, avCharHeight);
-
- graphics.setFont(av.getFont());
- }
-
- y1 += avCharHeight - avCharHeight / 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 = ' ';
- boolean srep = av.isDisplayReferenceSeq();
- for (int i = start; i <= end; i++)
- {
- graphics.setColor(Color.black);
-
- s = seq.getCharAt(i);
- if (!renderGaps && 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())
- {
- s = getDisplayChar(srep, 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(srep, i, s,
- '.');
-
- }
- }
-
- if (av.isUpperCasebold())
- {
- 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 = (avCharWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + avCharWidth
- * (i - start), y1);
- }
-
- }
-
- private char getDisplayChar(final boolean usesrep, int position,
- char s, char c)
- {
- // TODO - use currentSequenceGroup rather than alignemnt
- // currentSequenceGroup.getConsensus()
- char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().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 avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();
- int pady = avCharHeight / 5;
- int charOffset = 0;
- graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, avCharWidth * (end - start + 1), avCharHeight);
- 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 = (avCharWidth - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + x1
- + avCharWidth * (i - start), y1 + avCharHeight - pady);
- }
- }
- }
-
- public void drawCursor(SequenceI seq, int res, int x1, int y1)
- {
- int pady = av.getCharHeight() / 5;
- int charOffset = 0;
- graphics.setColor(Color.black);
- graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
- graphics.setColor(Color.white);
-
- graphics.setColor(Color.white);
-
- char s = seq.getCharAt(res);
- if (av.validCharWidth)
- {
-
- charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
- graphics.drawString(String.valueOf(s), charOffset + x1,
- (y1 + av.getCharHeight()) - pady);
- }
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview 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 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.api.FeatureRenderer;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.schemes.ColourSchemeI;\r
+import jalview.util.Comparison;\r
+\r
+import java.awt.Color;\r
+import java.awt.Font;\r
+import java.awt.FontMetrics;\r
+import java.awt.Graphics;\r
+\r
+public class SequenceRenderer implements jalview.api.SequenceRenderer\r
+{\r
+ AlignViewport av;\r
+\r
+ FontMetrics fm;\r
+\r
+ boolean renderGaps = true;\r
+\r
+ SequenceGroup currentSequenceGroup = null;\r
+\r
+ SequenceGroup[] allGroups = null;\r
+\r
+ Color resBoxColour;\r
+\r
+ Graphics graphics;\r
+\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\r
+ * 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.getAlignment().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.getGlobalColourScheme(), seq, i);\r
+ }\r
+\r
+ return resBoxColour;\r
+ }\r
+\r
+ /**\r
+ * Get the residue colour at the given sequence position - as determined by\r
+ * the sequence group colour (if any), else the colour scheme, possibly\r
+ * overridden by a feature colour.\r
+ * \r
+ * @param seq\r
+ * @param position\r
+ * @param fr\r
+ * @return\r
+ */\r
+ @Override\r
+ public Color getResidueColour(final SequenceI seq, int position,\r
+ FeatureRenderer fr)\r
+ {\r
+ // TODO replace 8 or so code duplications with calls to this method\r
+ // (refactored as needed)\r
+ Color col = getResidueBoxColour(seq, position);\r
+\r
+ if (fr != null)\r
+ {\r
+ col = fr.findFeatureColour(col, seq, position);\r
+ }\r
+ return col;\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, seq);\r
+ }\r
+ else if (forOverview && !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.getAlignment().findAllGroups(seq);\r
+ drawBoxes(seq, i, i, 0);\r
+ return resBoxColour;\r
+ }\r
+\r
+ public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,\r
+ 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.getCharWidth(), avCharWidth = av.getCharWidth(), avCharHeight = av\r
+ .getCharHeight();\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(avCharWidth * (curStart - start), y1, curWidth,\r
+ avCharHeight);\r
+ }\r
+ graphics.setColor(resBoxColour);\r
+\r
+ curStart = i;\r
+ curWidth = avCharWidth;\r
+ tempColour = resBoxColour;\r
+\r
+ }\r
+ else\r
+ {\r
+ curWidth += avCharWidth;\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ graphics.fillRect(avCharWidth * (curStart - start), y1, curWidth,\r
+ avCharHeight);\r
+ }\r
+\r
+ public void drawText(SequenceI seq, int start, int end, int y1)\r
+ {\r
+ int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();\r
+ Font boldFont = null;\r
+ boolean bold = false;\r
+ if (av.isUpperCasebold())\r
+ {\r
+ boldFont = new Font(av.getFont().getName(), Font.BOLD, avCharHeight);\r
+\r
+ graphics.setFont(av.getFont());\r
+ }\r
+\r
+ y1 += avCharHeight - avCharHeight / 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
+ boolean srep = av.isDisplayReferenceSeq();\r
+ for (int i = start; i <= end; i++)\r
+ {\r
+ graphics.setColor(Color.black);\r
+\r
+ s = seq.getCharAt(i);\r
+ if (!renderGaps && 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
+ if (currentSequenceGroup.getShowNonconserved())\r
+ {\r
+ s = getDisplayChar(srep, i, s,\r
+ '.');\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
+ if (av.getShowUnconserved())\r
+ {\r
+ s = getDisplayChar(srep, i, s,\r
+ '.');\r
+\r
+ }\r
+ }\r
+\r
+ if (av.isUpperCasebold())\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 = (avCharWidth - fm.charWidth(s)) / 2;\r
+ graphics.drawString(String.valueOf(s), charOffset + avCharWidth\r
+ * (i - start), y1);\r
+ }\r
+\r
+ }\r
+\r
+ private char getDisplayChar(final boolean usesrep, int position,\r
+ char s, char c)\r
+ {\r
+ // TODO - use currentSequenceGroup rather than alignemnt \r
+ // currentSequenceGroup.getConsensus()\r
+ char conschar = (usesrep) ? av.getAlignment().getSeqrep().getCharAt(position) : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter\r
+ .charAt(0);\r
+ if (conschar != '-' && s == conschar)\r
+ {\r
+ s = c;\r
+ }\r
+ return s;\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\r
+ && 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,\r
+ int x1, int y1)\r
+ {\r
+ int avCharWidth = av.getCharWidth(), avCharHeight = av.getCharHeight();\r
+ int pady = avCharHeight / 5;\r
+ int charOffset = 0;\r
+ graphics.setColor(Color.black);\r
+ graphics.fillRect(x1, y1, avCharWidth * (end - start + 1), avCharHeight);\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 = (avCharWidth - fm.charWidth(s)) / 2;\r
+ graphics.drawString(String.valueOf(s), charOffset + x1\r
+ + avCharWidth * (i - start), y1 + avCharHeight - pady);\r
+ }\r
+ }\r
+ }\r
+\r
+ public void drawCursor(SequenceI seq, int res, int x1, int y1)\r
+ {\r
+ int pady = av.getCharHeight() / 5;\r
+ int charOffset = 0;\r
+ graphics.setColor(Color.black);\r
+ graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());\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.getCharWidth() - fm.charWidth(s)) / 2;\r
+ graphics.drawString(String.valueOf(s), charOffset + x1,\r
+ (y1 + av.getCharHeight()) - pady);\r
+ }\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff