-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-\r
-import java.awt.*;\r
-import java.util.*;\r
-\r
-public class SequenceRenderer implements RendererI\r
-{\r
- FontMetrics fm;\r
-\r
- public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) {\r
-\r
- Color c = cs.findColour(seq, seq.getSequence(i, i + 1), i, null);\r
- return c;\r
-\r
- }\r
-\r
-\r
- public void drawSequence(Graphics g,ColourSchemeI cs,SequenceI seq,int start, int end, int x1, int y1, double width, int height,boolean showScores, boolean displayBoxes, boolean displayText, boolean colourText,Vector freq, int seqnum) {\r
-\r
-\r
- if (displayBoxes)\r
- drawBoxes(g,cs,seq,start,end,x1,y1,(int)width, height,freq);\r
-\r
- if (displayText)\r
- {\r
- fm = g.getFontMetrics();\r
- drawText(g,cs,colourText,seq,start,end,x1,y1,(int)width,height);\r
- }\r
- }\r
-\r
- public void drawBoxes(Graphics g,ColourSchemeI cs, 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
- Color currentColor = Color.WHITE;\r
-\r
- int curStart = x1;\r
- int curWidth = width;\r
-\r
- // int threshold = 80;\r
-\r
- while (i <= end && i < length) {\r
- Color c = getResidueBoxColour(cs,seq,i);\r
-\r
- // Hashtable hash = (Hashtable)freq.elementAt(i-start);\r
- // String s = (String)hash.get("maxResidue");\r
- // int count = ((Integer)hash.get("maxCount")).intValue();\r
- // int max = ((Integer)hash.get("size")).intValue();\r
- // int nongap = ((Integer)hash.get("nongap")).intValue();\r
- // float frac = (float)(count*1.0/(1.0*nongap));\r
-\r
- //System.out.println("Frac/count/nongap " + frac + " " + count + " " + nongap);\r
- /* if (!seq.getSequence().substring(i,i+1).equals(s) ||\r
- s.equals("-") ||\r
- s.equals(".") ||\r
- s.equals(" "))\r
- {\r
- c = Color.white;\r
- } else {\r
- if (frac > 0.9) {\r
- c = Color.red;\r
- } else if (frac > 0.8) {\r
- c = Color.orange;\r
- } else if (frac > 0.7) {\r
- c = Color.pink;\r
- } else if (frac > 0.5) {\r
- c = Color.yellow;\r
- } else if (frac> 0.3) {\r
- c = Color.lightGray;\r
- }\r
- }*/\r
-\r
- if (c != currentColor || c != null)\r
- {\r
- g.fillRect(x1+width*(curStart-start),y1,curWidth,height);\r
-\r
- currentColor = c;\r
- g.setColor(c);\r
-\r
- curStart = i;\r
- curWidth = width;\r
- }\r
- else\r
- curWidth += width;\r
-\r
- i++;\r
- }\r
- g.fillRect(x1+width*(curStart-start),y1,curWidth,height);\r
- }\r
-\r
- public void drawText(Graphics g, ColourSchemeI cs, boolean colText, 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
- g.setColor(Color.black);\r
-\r
- char s;\r
- // Need to find the sequence position here.\r
- for (int i = start; i <= end; i++)\r
- {\r
- if (i < end && i < seq.getLength())\r
- s = seq.getSequence().charAt(i);\r
- else if(i<seq.getLength())\r
- s = seq.getSequence().charAt(i);\r
- else\r
- s = ' ';\r
-\r
- if (colText)\r
- {\r
- Color c = getResidueBoxColour(cs, seq, i);\r
- g.setColor(c.darker());\r
- }\r
-\r
- charOffset = (width - fm.charWidth(s))/2;\r
-\r
-\r
- g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);\r
- }\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.FeatureRenderer;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
+
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+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 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() && av
+ .getCharWidth() == dwidth);
+
+ 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;
+ }
+
+ /**
+ * 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.getCharAt(i), i, seq);
+ }
+ 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)
+ {
+ 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)
+ {
+ 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(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());
+
+ if (monospacedFont && av.getShowText() && allGroups.length == 0
+ && !av.getColourText() && av.getThresholdTextColour() == 0)
+ {
+ 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;
+ boolean isgrep = currentSequenceGroup != null ? currentSequenceGroup
+ .getSeqrep() == seq : false;
+ char sr_c;
+ 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;
+ }
+
+ if (inCurrentSequenceGroup(i))
+ {
+ if (!currentSequenceGroup.getDisplayText())
+ {
+ continue;
+ }
+
+ if (currentSequenceGroup.thresholdTextColour > 0
+ || currentSequenceGroup.getColourText())
+ {
+ getboxColour = true;
+ getBoxColour(currentSequenceGroup.cs, 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);
+ }
+ 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;
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
+
+ if (av.getShowBoxes())
+ {
+ graphics.setColor(resBoxColour.darker());
+ }
+ else
+ {
+ graphics.setColor(resBoxColour);
+ }
+ }
+
+ if (av.getThresholdTextColour() > 0)
+ {
+ if (!getboxColour)
+ {
+ getBoxColour(av.getGlobalColourScheme(), seq, i);
+ }
+
+ if (resBoxColour.getRed() + resBoxColour.getBlue()
+ + resBoxColour.getGreen() < av.getThresholdTextColour())
+ {
+ graphics.setColor(av.getTextColour2());
+ }
+ }
+ if (!isarep && av.getShowUnconserved())
+ {
+ s = getDisplayChar(srep, i, s, '.', currentSequenceGroup);
+
+ }
+
+ }
+
+ 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 ? av.getAlignment()
+ .getSeqrep().getCharAt(position)
+ : (currentGroup.getSeqrep() != null ? currentGroup.getSeqrep()
+ .getCharAt(position) : av.getAlignment().getSeqrep()
+ .getCharAt(position)))
+ : (currentGroup != null && currentGroup.getConsensus() != null) ? 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 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.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);
+ }
+ }
+ }
+
+ 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());
+
+ if (av.isValidCharWidth())
+ {
+ graphics.setColor(Color.white);
+
+ char s = seq.getCharAt(res);
+
+ 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