X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=a8a9a470f593acb6736b282ed4052cfec33a141d;hb=d187567c926fed31f9cd9bda0dc112bc4d1b1261;hp=7df91496894483b6ceec6c5f50602345162a6a45;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java index 7df9149..a8a9a47 100755 --- a/src/jalview/gui/SequenceRenderer.java +++ b/src/jalview/gui/SequenceRenderer.java @@ -1,130 +1,388 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program 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 2 + * of the License, or (at your option) any later version. + * + * This program 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 this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.gui; import jalview.datamodel.*; + import jalview.schemes.*; import java.awt.*; -import java.util.*; -public class SequenceRenderer implements RendererI +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class SequenceRenderer { - FontMetrics fm; - AlignViewport av; + 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(); - public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) { - Color c = Color.WHITE; + // If EPS graphics, stringWidth will be a double, not an int + double dwidth = fm.getStringBounds("M", g).getWidth(); - try{ - if (cs != null) - c = cs.findColour(seq, seq.getSequence(i, i + 1), i, null); - }catch(Exception ex) - { } + monospacedFont = + dwidth == fm.getStringBounds("|",g).getWidth() + && av.charWidth == (int)dwidth; - return c; - } + this.renderGaps = renderGaps; + } - 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,Vector freq, int seqnum,AlignViewport av) { - this.av = av; + public Color getResidueBoxColour(SequenceI seq, int i) + { + allGroups = av.alignment.findAllGroups(seq); - if (displayBoxes == true) { - drawBoxes(g,cs,seq,start,end,x1,y1,(int)width, height,freq); + if (inCurrentSequenceGroup(i)) + { + if (currentSequenceGroup.getDisplayBoxes()) + { + getBoxColour(currentSequenceGroup.cs, seq, i); + } + } + else if (av.getShowBoxes()) + { + getBoxColour(av.globalColourScheme, seq, i); + } + + return resBoxColour; } - if (displayText == true) { - fm = g.getFontMetrics(); - drawText(g,cs,seq,start,end,x1,y1,(int)width,height); + + + /** + * 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.getSequence(i, i + 1), i); + } + else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i))) + { + resBoxColour = Color.lightGray; + } + else + { + resBoxColour = Color.white; + } } - } - public void drawBoxes(Graphics g,ColourSchemeI cs, SequenceI seq,int start, int end, int x1, int y1, int width, int height,Vector freq) { - int i = start; - int length = seq.getLength(); + /** + * 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; - Color currentColor = Color.WHITE; + drawBoxes(seq, start, end, y1); - int curStart = x1; - int curWidth = width; + if (av.validCharWidth) + drawText(seq, start, end, y1); + } - // int threshold = 80; + /** + * 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) + { + int i = start; + int length = seq.getLength(); - while (i <= end && i < length) { - Color c = getResidueBoxColour(cs,seq,i); + int curStart = -1; + int curWidth = av.charWidth; - // Hashtable hash = (Hashtable)freq.elementAt(i-start); - // String s = (String)hash.get("maxResidue"); - // int count = ((Integer)hash.get("maxCount")).intValue(); - // int max = ((Integer)hash.get("size")).intValue(); - // int nongap = ((Integer)hash.get("nongap")).intValue(); - // float frac = (float)(count*1.0/(1.0*nongap)); + Color tempColour = null; - //System.out.println("Frac/count/nongap " + frac + " " + count + " " + nongap); - /* if (!seq.getSequence().substring(i,i+1).equals(s) || - s.equals("-") || - s.equals(".") || - s.equals(" ")) - { - c = Color.white; - } else { - if (frac > 0.9) { - c = Color.red; - } else if (frac > 0.8) { - c = Color.orange; - } else if (frac > 0.7) { - c = Color.pink; - } else if (frac > 0.5) { - c = Color.yellow; - } else if (frac> 0.3) { - c = Color.lightGray; - } - }*/ - - if (c != currentColor || c != null) + while (i <= end) { - g.fillRect(x1+width*(curStart-start),y1,curWidth,height); + resBoxColour = Color.white; + + if (i < length) + { + if (inCurrentSequenceGroup(i)) + { + if (currentSequenceGroup.getDisplayBoxes()) + { + getBoxColour(currentSequenceGroup.cs, seq, i); + } + } + else if (av.getShowBoxes()) + { + getBoxColour(av.globalColourScheme, seq, i); + } + + } + + if (resBoxColour != tempColour) + { + if (tempColour != null) + { + graphics.fillRect( av.charWidth * (curStart - start), y1, + curWidth, av.charHeight); + } + + graphics.setColor(resBoxColour); - currentColor = c; - g.setColor(c); + curStart = i; + curWidth = av.charWidth; + tempColour = resBoxColour; + } + else + { + curWidth += av.charWidth; + } - curStart = i; - curWidth = width; + i++; } - else - curWidth += width; - i++; + graphics.fillRect( av.charWidth * (curStart - start), y1, curWidth, + av.charHeight); + } - g.fillRect(x1+width*(curStart-start),y1,curWidth,height); - } - - public void drawText(Graphics g, ColourSchemeI cs, SequenceI seq,int start, int end, int x1, int y1, int width, int height) - { - int pady = height/5; - int charOffset=0; - g.setColor(Color.black); - boolean colourText = av.getColourText(); - Color c; - char s; - // Need to find the sequence position here. - for (int i = start; i <= end; i++) + + /** + * 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) { - if (i < end && i < seq.getLength()) - s = seq.getSequence().charAt(i); - else if(i=seq.getLength()) + end = seq.getLength()-1; + graphics.setColor(Color.black); + + + if(monospacedFont && av.showText && allGroups.length==0 && !av.getColourText()) + { + if(av.renderGaps) + graphics.drawString(seq.getSequence(start, end + 1), 0, y1); + else + { + char gap = av.getGapCharacter(); + graphics.drawString( seq.getSequence(start, end+1).replace(gap, ' '), 0, y1); + } + } else - 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()); + } + } + else + { + if (!av.getShowText()) + { + continue; + } + + if (av.getColourText()) + { + getBoxColour(av.globalColourScheme, seq, i); + + if (av.getShowBoxes()) + { + graphics.setColor(resBoxColour.darker()); + } + else + { + graphics.setColor(resBoxColour); + } + } + } + + charOffset = (av.charWidth - fm.charWidth(s)) / 2; + + // System.out.print(s); + graphics.drawString(String.valueOf(s), + charOffset + av.charWidth * (i - start), + y1); + + } + // System.out.println("\n"); + } + } + + /** + * DOCUMENT ME! + * + * @param res DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + boolean inCurrentSequenceGroup(int res) + { + if (allGroups == null) + { + return false; + } - if (colourText) + for (int i = 0; i < allGroups.length; i++) { - c = getResidueBoxColour(cs, seq, i); - g.setColor(c.darker()); + if ((allGroups[i].getStartRes() <= res) && + (allGroups[i].getEndRes() >= res)) + { + currentSequenceGroup = allGroups[i]; + + return true; + } } - charOffset = (width - fm.charWidth(s))/2; + 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.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.getSequence().charAt(i); + } - g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady); + 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); + + if(av.validCharWidth) + { + graphics.setColor(Color.white); + + char s = seq.getCharAt(res); + + charOffset = (av.charWidth - fm.charWidth(s)) / 2; + graphics.drawString(String.valueOf(s), + charOffset + x1, + (y1 + av.charHeight) - pady); + } + + } }