From a18b1693a979b106bc629865d27a8cbb5b16971d Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Thu, 18 Nov 2004 18:47:34 +0000 Subject: [PATCH] not used at present --- src/jalview/gui/BlockRenderer.java | 136 ---------------------------------- src/jalview/gui/CpGRenderer.java | 87 ---------------------- src/jalview/gui/FeatureRenderer.java | 85 --------------------- src/jalview/gui/GraphRenderer.java | 128 -------------------------------- 4 files changed, 436 deletions(-) delete mode 100755 src/jalview/gui/BlockRenderer.java delete mode 100755 src/jalview/gui/CpGRenderer.java delete mode 100755 src/jalview/gui/FeatureRenderer.java delete mode 100755 src/jalview/gui/GraphRenderer.java diff --git a/src/jalview/gui/BlockRenderer.java b/src/jalview/gui/BlockRenderer.java deleted file mode 100755 index 1dca1c4..0000000 --- a/src/jalview/gui/BlockRenderer.java +++ /dev/null @@ -1,136 +0,0 @@ -package jalview.gui; - -import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.analysis.*; -import jalview.util.*; -import java.awt.*; -import java.util.*; - -public class BlockRenderer implements RendererI { - protected Color color = Color.black; - protected Color maroon = new Color(200,0,50); - protected Color purple = new Color(255,100,255); - - public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) { - Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null); - return c; - } - - 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 pid, int seqnum,AlignViewport av) { - -/* int i = start; - int length = seq.getLength(); - - Color currentColor = Color.white; - Vector kmers = av.getKmers(); - - g.setColor(Color.black); - - int prev = -1; - - int seqno = -1; - - for (int ii = 0; ii < av.getAlignment().getHeight(); ii++) { - if (av.getSelection().contains(av.getAlignment().getSequenceAt(ii))) { - seqno = ii; - } - } - - int blstart = start - 20; - int blend = end + 20; - - if (blstart < 0) { - blstart = 0; - } - - if (blend > av.getAlignment().getWidth()) { - blend = av.getAlignment().getWidth(); - } - - Hashtable blocks = AAFrequency.findBlocks(av.getAlignment().getSequences(), - blstart, - blend, - av.getSelection().asVector()); - - Hashtable hkmer = AlignmentUtil.findKmers(seq,blstart,blend,kmers); - - boolean inblock = false; - - int bstart = -1; - int blen = -1; - int klen = -1; - int block_end = -1; - Color bc; - - // System.out.println("Rendering " + start + " " + end); - - while (i <= blend && i < length) { - boolean foundblock = false; - - if (blocks.get(new Integer(i-blstart)) != null) { - - blen = ((Integer)blocks.get(new Integer(i-blstart))).intValue(); - - foundblock = true; - - block_end = i + blen-1; - - g.setColor(getColor(blen)); - g.fillRect(x1+(int)(width*(i-start)),y1, - (int)width+1, height/2); - } - - boolean foundKmer = false; - - if (hkmer.get(new Integer(i-blstart)) != null) { - - - klen = ((Integer)hkmer.get(new Integer(i-blstart))).intValue(); - - // System.out.println("Got kmer " + i + " " + start + " kength " + klen); - - foundKmer = true; - - g.setColor(Color.lightGray); - - if ((int)width> 5) { - g.fillRect(x1+(int)(width*(i-start)),y1+height/2, - (int)(width*klen)+1, height/2); - } else { - g.fillRect(x1+(int)(width*(i-start)),y1+height/2, - (int)(width*klen)+1, height/2); - - } - - } - - if (width > 5) { - g.setColor(Color.black); - g.drawString(seq.getSequence().substring(i,i+1),x1+(int)(width*(i-start)),y1+height); - } - i++; - }*/ - } - - public Color getColor(int blen) { - - Color bc; - - if (blen > 20 ) { - bc = Color.yellow; - }else if (blen > 10) { - bc = Color.red; - } else if (blen > 5) { - bc = Color.blue; - } else if (blen > 2) { - bc = purple; - } else if (blen == 2) { - bc = Color.orange; - - } else { - bc = Color.lightGray; - } - return bc; - } -} diff --git a/src/jalview/gui/CpGRenderer.java b/src/jalview/gui/CpGRenderer.java deleted file mode 100755 index b5dc128..0000000 --- a/src/jalview/gui/CpGRenderer.java +++ /dev/null @@ -1,87 +0,0 @@ -package jalview.gui; -import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.util.*; -import jalview.analysis.*; -import java.awt.*; -import java.awt.geom.*; -import java.util.*; - -public class CpGRenderer implements RendererI { - protected Color color = Color.black; - - public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) { - Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null); - return c; - } - - 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 pid, int seqnum,AlignViewport av) { - - int i = start; - int length = seq.getLength(); - - Color currentColor = Color.white; - - g.setColor(Color.black); - - int window = 1000; - int max = window/5; - - int step = window/10; - - if (step > window) { - step = window; - } - - if (window < 2) { - window = 2; - step = 1; - } - - int cpgstart = start; - int cpgend = end; - - if (cpgstart <= window/2 ) { - cpgstart = window/2; - } - if (cpgend+window/2 >= length) { - cpgend = length-window/2; - } - - Hashtable vals = AAFrequency.findKmerCount(seq,cpgstart,cpgend,window,step,av.getKmers()); - - Enumeration en = vals.keys(); - - Vector valset = new Vector(); - - while (en.hasMoreElements()) { - valset.add((Integer)en.nextElement()); - } - Collections.sort(valset); - - g.setColor(Color.black); - - int j = 0; - - while (j < valset.size()) { - - Integer posInt = (Integer)valset.elementAt(j); - int count = ((Integer)vals.get(posInt)).intValue(); - int pos = posInt.intValue(); - - if (count > 40) { - g.setColor(Color.red); - } else { - g.setColor(Color.black); - } - - g.fillRect(x1 + (int)(width*(pos-start-width/2)), - y1+height - (int)(count*height/max), - (int)(step*width), - (int)(count*height/max)); - - j++; - } - } - -} diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java deleted file mode 100755 index cd754c7..0000000 --- a/src/jalview/gui/FeatureRenderer.java +++ /dev/null @@ -1,85 +0,0 @@ -package jalview.gui; - -import jalview.datamodel.*; -import jalview.schemes.*; -import java.awt.*; -import java.util.*; - -public class FeatureRenderer implements RendererI { - - - public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) { - Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null); - return c; - } - - 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 pid, int seqnum,AlignViewport av) { - - int i = start; - int length = seq.getLength(); - - Color currentColor = Color.black; - - - int prev = -1; - int fstart = 0; - char prevc = '-'; - - g.setColor(Color.magenta); - - while (i <= end && i < length) { - char c = seq.getCharAt(i); - if (c != '-') { - - if (prevc != c) { - - if (prevc == 'F') { - g.setColor(Color.green); - } else if (prevc == 'R') { - g.setColor(Color.cyan); - } else if (prevc == 'M') { - g.setColor(Color.magenta); - } else if (prevc == 'P') { - g.setColor(Color.yellow); - } - g.fillRect(x1+(int)(width*(i-fstart)),y1+height/4,(int)((prev-fstart+1)*width),height/2); - - prevc = c; - fstart = i; - } - } else if (prevc != '-') { - if (prevc == 'F') { - g.setColor(Color.green); - } else if (prevc == 'R') { - g.setColor(Color.cyan); - } else if (prevc == 'M') { - g.setColor(Color.magenta); - } else if (prevc == 'P') { - g.setColor(Color.yellow); - } - g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((i-fstart+1)*width),height/2); - - prevc = c; - } else { - fstart = -1; - } - i++; - } - - if (fstart != -1) { - if (prevc == 'F') { - g.setColor(Color.green); - } else if (prevc == 'R') { - g.setColor(Color.cyan); - } else if (prevc == 'M') { - g.setColor(Color.magenta); - } else if (prevc == 'P') { - g.setColor(Color.yellow); - } - - //g.fillRect(x1+(int)(width*(fstart-start)),y1+height/4,(int)((end-fstart+1)*width),height/2); - - } - } - -} diff --git a/src/jalview/gui/GraphRenderer.java b/src/jalview/gui/GraphRenderer.java deleted file mode 100755 index e7d1757..0000000 --- a/src/jalview/gui/GraphRenderer.java +++ /dev/null @@ -1,128 +0,0 @@ -package jalview.gui; - -import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.util.*; - -import java.awt.*; -import java.awt.geom.*; -import java.util.*; - -public class GraphRenderer implements RendererI { - protected Color color = Color.black; - protected Color maroon = new Color(200,0,50); - - public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i) { - Color c = cs.findColour(seq,seq.getSequence(i,i+1),i,null); - return c; - } - - 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 pid, int seqnum,AlignViewport av) { - - int i = start; - int length = seq.getLength(); - - Color currentColor = Color.white; - - g.setColor(Color.black); - - int prev = -1; - - while (i <= end && i < length) { - char c = seq.getCharAt(i); - - if (c != '-') { - Vector values = (Vector)pid.elementAt(i-start); - int val = ((Integer)values.elementAt(seqnum)).intValue(); - - int frac = (int)(100*val/(av.getPIDWindow()+1)); - -// if (frac > 95) { - // g.setColor(maroon); - // } else if (frac > 90) { -// g.setColor(Color.red); -// } else if (frac > 80) { -// g.setColor(Color.orange); -// } else if (frac > 70) { -// g.setColor(Color.pink); -// } else if (frac > 50) { -// g.setColor(Color.yellow); -// } else if (frac > 30) { -// g.setColor(Color.lightGray); -// } - - int baseline = av.getPIDBaseline(); - - frac -= baseline; - - if (frac < 0) { - frac = 0; - } - if (baseline == 100) { - baseline = 99; - } - - Graphics2D g2d = (Graphics2D)g; - - g2d.setColor(new Color(255*frac/(100-baseline),50*frac/(100-baseline),50*frac/(100-baseline))); - - //g.setColor(new Color(255*frac/(100-baseline),50*frac/(100-baseline),255-50*frac/(100-baseline))); - //g.fillRect(x1+(int)(width*(i-start)),y1+height - (int)(frac*height/(100-baseline)), - //width, (int)(frac*height/(100-baseline))); - - int[] xpoints = new int[4]; - int[] ypoints = new int[4]; - - if (prev == -1) { - prev = y1 + height - (int)(frac*height/(100-baseline)); - } - - // 1----2 - // | | - // 4----3 - - xpoints[0] = (x1+ (int)(width*(i-start))); - ypoints[0] = prev; - - xpoints[1] = (x1 + (int)(width*(i-start+1))); - ypoints[1] = y1 + height - (int)(frac*height/(100-baseline)); - - xpoints[3] = (x1 + (int)(width*(i-start)));; - ypoints[3] = y1 + height; - - xpoints[2] = (x1 + (int)(width*(i-start+1))); - ypoints[2] = y1 + height; - - Polygon poly = new Polygon(); - - poly.xpoints = xpoints; - poly.ypoints = ypoints; - poly.npoints = 4; - - g2d.fill(poly); - - if (width > 5) { - g.setColor(Color.black); - g.drawString(seq.getSequence().substring(i,i+1),x1+(int)(width*(i-start)),y1+height); - } else { - g.setColor(Color.black); - - if (prev != -1) { - - g.drawLine(x1+(int)(width*(i-start)-width/2), prev, - x1+(int)(width*(i-start+1)-width/2),y1+height - (int)(frac*height/(100-baseline))); - } else { - g.drawLine(x1+(int)(width*(i-start)), y1+height - (int)(frac*height/(100-baseline)), - x1+(int)(width*(i-start+1)),y1+height - (int)(frac*height/(100-baseline))); - } - - } - prev = ypoints[1]; - } else { - prev = -1; - } - i++; - } - } - -} -- 1.7.10.2