-/*\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
-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
-\r
- public SequenceRenderer(AlignViewport av)\r
- {\r
- this.av = av;\r
- }\r
-\r
- public void renderGaps(boolean b)\r
- {\r
- renderGaps = b;\r
- }\r
-\r
- public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
- {\r
- getBoxColour(cs, seq, i);\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.getSequence(i, i + 1), i);\r
- }\r
- else\r
- {\r
- resBoxColour = Color.white;\r
- }\r
- }\r
-\r
- public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
- int start, int end, int x1, int y1, int width,\r
- int height)\r
- {\r
- allGroups = sg;\r
-\r
- graphics = g;\r
-\r
- drawBoxes(seq, start, end, x1, y1, (int) width, height);\r
-\r
- fm = g.getFontMetrics();\r
- drawText(seq, start, end, x1, y1, (int) width, height);\r
-\r
- }\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
- while (i <= end && i < length)\r
- {\r
- if (inCurrentSequenceGroup(i))\r
- {\r
- if (currentSequenceGroup.getDisplayBoxes())\r
- {\r
- getBoxColour(currentSequenceGroup.cs, seq, i);\r
- }\r
- else\r
- {\r
- resBoxColour = Color.white;\r
- }\r
- }\r
- else if (av.getShowBoxes())\r
- {\r
- getBoxColour(av.getGlobalColourScheme(), seq, i);\r
- }\r
- else\r
- {\r
- resBoxColour = Color.white;\r
- }\r
-\r
- if (resBoxColour != tempColour)\r
- {\r
- if (tempColour != null)\r
- {\r
- graphics.fillRect(x1 + width * (curStart - start), y1, curWidth,\r
- height);\r
- }\r
- graphics.setColor(resBoxColour);\r
-\r
- curStart = i;\r
- curWidth = width;\r
- tempColour = resBoxColour;\r
-\r
- }\r
- else\r
- {\r
- curWidth += width;\r
- }\r
-\r
- i++;\r
- }\r
-\r
- graphics.fillRect(x1 + width * (curStart - start), y1, curWidth, height);\r
- }\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
- // Need to find the sequence position here.\r
-\r
- String sequence = seq.getSequence();\r
- for (int i = start; i <= end; i++)\r
- {\r
- graphics.setColor(Color.black);\r
- if (i < sequence.length())\r
- {\r
- s = sequence.charAt(i);\r
- }\r
- else\r
- {\r
- s = ' ';\r
- }\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
- 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 + width * (i - start),\r
- y1 + height - pady);\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, 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
- // 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),\r
- y1 + height - pady);\r
- }\r
- }\r
-\r
-}\r
+/*
+ * 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 java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+
+public class SequenceRenderer implements jalview.api.SequenceRenderer
+{
+ final static int CHAR_TO_UPPER = 'A' - 'a';
+
+ 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;
+ }
+
+ @Override
+ 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
+ && !jalview.util.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 && 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())
+ {
+ s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
+ }
+ }
+ 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, '.', null);
+
+ }
+ }
+
+ 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);
+ }
+
+ }
+
+ /**
+ * Returns 'conservedChar' to represent the given position if the sequence
+ * character at that position is equal to the consensus (ignoring case), else
+ * returns the sequence character
+ *
+ * @param usesrep
+ * @param position
+ * @param sequenceChar
+ * @param conservedChar
+ * @return
+ */
+ private char getDisplayChar(final boolean usesrep, int position,
+ char sequenceChar, char conservedChar, SequenceGroup currentGroup)
+ {
+ // TODO - use currentSequenceGroup rather than alignment
+ // currentSequenceGroup.getConsensus()
+ char conschar = (usesrep) ? (currentGroup == null
+ || position < currentGroup.getStartRes()
+ || position > currentGroup.getEndRes() ? av.getAlignment()
+ .getSeqrep().getCharAt(position)
+ : (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
+ .getCharAt(position) : av.getAlignment().getSeqrep()
+ .getCharAt(position)))
+ : (currentGroup != null && currentGroup.getConsensus() != null
+ && position >= currentGroup.getStartRes()
+ && position <= currentGroup.getEndRes() && currentGroup
+ .getConsensus().annotations.length > position) ? currentGroup
+ .getConsensus().annotations[position].displayCharacter
+ .charAt(0)
+ : av.getAlignmentConsensusAnnotation().annotations[position].displayCharacter
+ .charAt(0);
+ if (!jalview.util.Comparison.isGap(conschar)
+ && (sequenceChar == conschar || sequenceChar + CHAR_TO_UPPER == conschar))
+ {
+ sequenceChar = conservedChar;
+ }
+ return sequenceChar;
+ }
+
+ 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);
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff