-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import java.awt.*;\r
-import java.util.*;\r
-\r
-public class SequenceRenderer implements RendererI\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
-\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
- resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i, av.getConsensus(false));\r
- else\r
- resBoxColour = Color.white;\r
- }\r
-\r
- public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)\r
- {\r
- allGroups = sg;\r
-\r
- graphics = g;\r
-\r
- drawBoxes(seq, start, end, x1, y1, (int) width, height, pid);\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, int width, int height,Vector freq) {\r
- int i = start;\r
- int length = seq.getLength();\r
-\r
- int curStart = x1;\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
- getBoxColour(currentSequenceGroup.cs, seq, i);\r
- }\r
- else if(av.getShowBoxes())\r
- getBoxColour(av.getGlobalColourScheme(), seq, i);\r
- else\r
- resBoxColour = Color.white;\r
-\r
-\r
- if (resBoxColour != tempColour)\r
- {\r
- graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);\r
- graphics.setColor(resBoxColour);\r
-\r
- curStart = i;\r
- curWidth = width;\r
- tempColour = resBoxColour;\r
-\r
- }\r
- else\r
- curWidth += width;\r
-\r
- i++;\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, 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
- graphics.setColor(Color.black);\r
- String sequence = seq.getSequence();\r
- for (int i = start; i <= end; i++)\r
- {\r
- if(i<sequence.length())\r
- s = sequence.charAt(i);\r
- else\r
- s = ' ';\r
-\r
- if(!renderGaps && jalview.util.Comparison.isGap(s))\r
- continue;\r
-\r
-\r
- if (inCurrentSequenceGroup(i))\r
- {\r
- if(!currentSequenceGroup.getDisplayText())\r
- continue;\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
- continue;\r
-\r
- if(av.getColourText())\r
- {\r
- getBoxColour(av.getGlobalColourScheme(), seq, i);\r
- if(av.getShowBoxes())\r
- graphics.setColor(resBoxColour.darker());\r
- else\r
- graphics.setColor(resBoxColour);\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
-\r
- boolean inCurrentSequenceGroup(int res)\r
- {\r
- if(allGroups ==null)\r
- return false;\r
-\r
- for(int i=0; i<allGroups.length; i++)\r
- if(allGroups[i].getStartRes()<=res && allGroups[i].getEndRes()>=res)\r
- {\r
- currentSequenceGroup = allGroups[i];\r
- return true;\r
- }\r
-\r
- return false;\r
- }\r
-\r
- public void drawHighlightedText(SequenceI seq,int start, int end, int x1, 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
- s = seq.getSequence().charAt(i);\r
-\r
- charOffset = (width - fm.charWidth(s))/2;\r
- graphics.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);\r
- }\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.gui;
+
+import jalview.api.AlignViewportI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueColourFinder;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+
+import org.jfree.graphics2d.svg.SVGGraphics2D;
+import org.jibble.epsgraphics.EpsGraphics2D;
+
+public class SequenceRenderer implements jalview.api.SequenceRenderer
+{
+ final static int CHAR_TO_UPPER = 'A' - 'a';
+
+ AlignViewportI av;
+
+ FontMetrics fm;
+
+ boolean renderGaps = true;
+
+ SequenceGroup[] allGroups = null;
+
+ // Color resBoxColour;
+
+ Graphics graphics;
+
+ boolean monospacedFont;
+
+ ResidueColourFinder resColourFinder;
+
+ /**
+ * Creates a new SequenceRenderer object
+ *
+ * @param viewport
+ */
+ public SequenceRenderer(AlignViewportI viewport)
+ {
+ this.av = viewport;
+ resColourFinder = new ResidueColourFinder();
+ }
+
+ /**
+ * 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()
+ && av.getCharWidth() == dwidth);
+
+ this.renderGaps = renderGaps;
+ }
+
+ /**
+ * 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 finder
+ * @return
+ */
+ @Override
+ public Color getResidueColour(final SequenceI seq, int position,
+ FeatureColourFinder finder)
+ {
+ allGroups = av.getAlignment().findAllGroups(seq);
+ return resColourFinder.getResidueColour(av.getShowBoxes(),
+ av.getResidueShading(), allGroups, seq, position, finder);
+ }
+
+ /**
+ * 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.isValidCharWidth())
+ {
+ 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)
+ {
+ Color resBoxColour = Color.white;
+
+ if (seq == null)
+ {
+ return; // fix for racecondition
+ }
+ int i = start;
+ int length = seq.getLength();
+
+ int curStart = -1;
+ int curWidth = av.getCharWidth(), avWidth = av.getCharWidth(),
+ avHeight = av.getCharHeight();
+
+ Color tempColour = null;
+
+ while (i <= end)
+ {
+ resBoxColour = Color.white;
+
+ if (i < length)
+ {
+ SequenceGroup currentSequenceGroup = resColourFinder
+ .getCurrentSequenceGroup(allGroups, i);
+ if (currentSequenceGroup != null)
+ {
+ if (currentSequenceGroup.getDisplayBoxes())
+ {
+ resBoxColour = resColourFinder.getBoxColour(
+ currentSequenceGroup.getGroupColourScheme(), seq, i);
+ }
+ }
+ else if (av.getShowBoxes())
+ {
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
+ }
+ }
+
+ if (resBoxColour != tempColour)
+ {
+ if (tempColour != null)
+ {
+ graphics.fillRect(avWidth * (curStart - start), y1, curWidth,
+ avHeight);
+ }
+
+ graphics.setColor(resBoxColour);
+
+ curStart = i;
+ curWidth = avWidth;
+ tempColour = resBoxColour;
+ }
+ else
+ {
+ curWidth += avWidth;
+ }
+
+ i++;
+ }
+
+ graphics.fillRect(avWidth * (curStart - start), y1, curWidth, avHeight);
+
+ }
+
+ /**
+ * 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.getCharHeight() - av.getCharHeight() / 5; // height/5 replaces pady
+ int charOffset = 0;
+ char s;
+
+ if (end + 1 >= seq.getLength())
+ {
+ end = seq.getLength() - 1;
+ }
+ graphics.setColor(av.getTextColour());
+
+ boolean drawAllText = monospacedFont && av.getShowText()
+ && allGroups.length == 0 && !av.getColourText()
+ && av.getThresholdTextColour() == 0;
+
+ /*
+ * EPS or SVG misaligns monospaced strings (JAL-3239)
+ * so always draw these one character at a time
+ */
+ if (graphics instanceof EpsGraphics2D
+ || graphics instanceof SVGGraphics2D)
+ {
+ drawAllText = false;
+ }
+ if (drawAllText)
+ {
+ if (av.isRenderGaps())
+ {
+ graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
+ }
+ else
+ {
+ char gap = av.getGapCharacter();
+ graphics.drawString(
+ seq.getSequenceAsString(start, end + 1).replace(gap, ' '),
+ 0, y1);
+ }
+ }
+ else
+ {
+ boolean srep = av.isDisplayReferenceSeq();
+ boolean getboxColour = false;
+ boolean isarep = av.getAlignment().getSeqrep() == seq;
+ Color resBoxColour = Color.white;
+
+ for (int i = start; i <= end; i++)
+ {
+
+ graphics.setColor(av.getTextColour());
+ getboxColour = false;
+ s = seq.getCharAt(i);
+
+ if (!renderGaps && jalview.util.Comparison.isGap(s))
+ {
+ continue;
+ }
+
+ SequenceGroup currentSequenceGroup = resColourFinder
+ .getCurrentSequenceGroup(allGroups, i);
+ if (currentSequenceGroup != null)
+ {
+ if (!currentSequenceGroup.getDisplayText())
+ {
+ continue;
+ }
+
+ if (currentSequenceGroup.thresholdTextColour > 0
+ || currentSequenceGroup.getColourText())
+ {
+ getboxColour = true;
+ resBoxColour = resColourFinder.getBoxColour(
+ currentSequenceGroup.getGroupColourScheme(), seq, i);
+
+ if (currentSequenceGroup.getColourText())
+ {
+ graphics.setColor(resBoxColour.darker());
+ }
+
+ if (currentSequenceGroup.thresholdTextColour > 0)
+ {
+ if (resBoxColour.getRed() + resBoxColour.getBlue()
+ + resBoxColour
+ .getGreen() < currentSequenceGroup.thresholdTextColour)
+ {
+ graphics.setColor(currentSequenceGroup.textColour2);
+ }
+ }
+ }
+ else
+ {
+ graphics.setColor(currentSequenceGroup.textColour);
+ }
+ boolean isgrep = currentSequenceGroup != null
+ ? currentSequenceGroup.getSeqrep() == seq
+ : false;
+ if (!isarep && !isgrep
+ && currentSequenceGroup.getShowNonconserved()) // todo
+ // optimize
+ {
+ // todo - use sequence group consensus
+ s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
+
+ }
+
+ }
+ else
+ {
+ if (!av.getShowText())
+ {
+ continue;
+ }
+
+ if (av.getColourText())
+ {
+ getboxColour = true;
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
+
+ if (av.getShowBoxes())
+ {
+ graphics.setColor(resBoxColour.darker());
+ }
+ else
+ {
+ graphics.setColor(resBoxColour);
+ }
+ }
+
+ if (av.getThresholdTextColour() > 0)
+ {
+ if (!getboxColour)
+ {
+ resBoxColour = resColourFinder
+ .getBoxColour(av.getResidueShading(), seq, i);
+ }
+
+ if (resBoxColour.getRed() + resBoxColour.getBlue()
+ + resBoxColour.getGreen() < av.getThresholdTextColour())
+ {
+ graphics.setColor(av.getTextColour2());
+ }
+ }
+ if (!isarep && av.getShowUnconserved())
+ {
+ s = getDisplayChar(srep, i, s, '.', null);
+
+ }
+
+ }
+
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s),
+ charOffset + av.getCharWidth() * (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;
+ }
+
+ /**
+ * 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.getCharHeight() / 5;
+ int charOffset = 0;
+ graphics.setColor(Color.BLACK);
+ graphics.fillRect(x1, y1, av.getCharWidth() * (end - start + 1),
+ av.getCharHeight());
+ graphics.setColor(Color.white);
+
+ char s = '~';
+
+ // Need to find the sequence position here.
+ if (av.isValidCharWidth())
+ {
+ for (int i = start; i <= end; i++)
+ {
+ if (i < seq.getLength())
+ {
+ s = seq.getCharAt(i);
+ }
+
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+ graphics.drawString(String.valueOf(s),
+ charOffset + x1 + (av.getCharWidth() * (i - start)),
+ (y1 + av.getCharHeight()) - pady);
+ }
+ }
+ }
+
+ /**
+ * Draw a sequence canvas cursor
+ *
+ * @param g
+ * graphics context to draw on
+ * @param s
+ * character to draw at cursor
+ * @param x1
+ * x position of cursor in graphics context
+ * @param y1
+ * y position of cursor in graphics context
+ */
+ public void drawCursor(Graphics g, char s, int x1, int y1)
+ {
+ int pady = av.getCharHeight() / 5;
+ int charOffset = 0;
+ g.setColor(Color.black);
+ g.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight());
+
+ if (av.isValidCharWidth())
+ {
+ g.setColor(Color.white);
+ charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2;
+ g.drawString(String.valueOf(s), charOffset + x1,
+ (y1 + av.getCharHeight()) - pady);
+ }
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff