From 227daebd9bdf92c83712e077d958a690cdee0f7a Mon Sep 17 00:00:00 2001 From: janengelhardt Date: Mon, 8 Aug 2011 23:32:30 +0200 Subject: [PATCH] JAL-891; structure logo is adapted to two char's; Missing: calculate bp frequencies and include them in the draw-part; Change-Id: Ie43edd7a074f6b219c808fa2519d2b88659f30e5 --- src/jalview/analysis/StructureFrequency.java | 16 +- src/jalview/gui/AlignViewport.java | 196 +++++++++------- src/jalview/gui/AnnotationPanel.java | 319 +++++++++++++++----------- 3 files changed, 312 insertions(+), 219 deletions(-) diff --git a/src/jalview/analysis/StructureFrequency.java b/src/jalview/analysis/StructureFrequency.java index 8338c9d..b9c61c2 100644 --- a/src/jalview/analysis/StructureFrequency.java +++ b/src/jalview/analysis/StructureFrequency.java @@ -469,10 +469,15 @@ public class StructureFrequency * @return */ public static int[] extractProfile(Hashtable hconsensus, - boolean ignoreGapsInConsensusCalculation) + boolean ignoreGapsInConsensusCalculation, + int column) { - //System.out.println("StructureFrequency.extractProfile"); - int[] rtnval = new int[11]; + //TODO is there a more elegant way to acces the column number? + /* + * calculate the frequence of the 16 bp variations for this column + * 'somehow' transfer this via getProfile and let it correctly draw + */ + int[] rtnval = new int[22]; int[][] profile = (int[][]) hconsensus.get(StructureFrequency.PROFILE); if (profile == null) return null; @@ -493,10 +498,15 @@ public class StructureFrequency if (((char[]) ca[c])[0] != '-') { rtnval[rtnval[0]++] = ((char[]) ca[c])[0]; + //System.out.println("rtnval-"+c+": "+((char[]) ca[c])[0]); rtnval[rtnval[0]++] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 : 0]); } } + for(int i=0; i seqvectors = new ArrayList(); - for (PDBEntry pdb: pdbEntries) { - ArrayList seqs = new ArrayList(); - for (int i = 0; i < alignment.getHeight(); i++) - { - Vector pdbs = alignment.getSequenceAt(i) - .getDatasetSequence().getPDBId(); - if (pdbs == null) - continue; - SequenceI sq; - for (int p = 0; p < pdbs.size(); p++) + for (PDBEntry pdb : pdbEntries) + { + ArrayList seqs = new ArrayList(); + for (int i = 0; i < alignment.getHeight(); i++) { - PDBEntry p1 = (PDBEntry) pdbs.elementAt(p); - if (p1.getId().equals(pdb.getId())) + Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence() + .getPDBId(); + if (pdbs == null) + continue; + SequenceI sq; + for (int p = 0; p < pdbs.size(); p++) { - if (!seqs.contains(sq=alignment.getSequenceAt(i))) - seqs.add(sq); + PDBEntry p1 = (PDBEntry) pdbs.elementAt(p); + if (p1.getId().equals(pdb.getId())) + { + if (!seqs.contains(sq = alignment.getSequenceAt(i))) + seqs.add(sq); - continue; + continue; + } } } - } - seqvectors.add(seqs.toArray(new SequenceI[seqs.size()])); + seqvectors.add(seqs.toArray(new SequenceI[seqs.size()])); } return seqvectors.toArray(new SequenceI[seqvectors.size()][]); } diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index e42264d..1acc0ca 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -94,9 +94,10 @@ public class AnnotationPanel extends JPanel implements MouseListener, boolean mouseDragging = false; boolean MAC = false; - - //for editing cursor + + // for editing cursor int cursorX = 0; + int cursorY = 0; /** @@ -146,7 +147,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public int adjustPanelHeight() { - int height=calcPanelHeight(); + int height = calcPanelHeight(); this.setPreferredSize(new Dimension(1, height)); if (ap != null) { @@ -158,8 +159,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, } /** - * calculate the height for visible annotation, revalidating bounds where necessary - * ABSTRACT GUI METHOD + * calculate the height for visible annotation, revalidating bounds where + * necessary ABSTRACT GUI METHOD + * * @return total height of annotation */ public int calcPanelHeight() @@ -463,17 +465,20 @@ public class AnnotationPanel extends JPanel implements MouseListener, /* * Just display the needed structure options */ - if(av.alignment.isNucleotide()==true){ - item = new JMenuItem(STEM); - item.addActionListener(this); - pop.add(item); - }else{ - item = new JMenuItem(HELIX); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(SHEET); - item.addActionListener(this); - pop.add(item); + if (av.alignment.isNucleotide() == true) + { + item = new JMenuItem(STEM); + item.addActionListener(this); + pop.add(item); + } + else + { + item = new JMenuItem(HELIX); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(SHEET); + item.addActionListener(this); + pop.add(item); } item = new JMenuItem(LABEL); item.addActionListener(this); @@ -667,35 +672,39 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void mouseClicked(MouseEvent evt) { - if(activeRow !=-1){ - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - AlignmentAnnotation anot = aa[activeRow]; - - if(anot.description.equals("secondary structure")){ - //System.out.println(anot.description+" "+anot.getRNAStruc()); - } - } + if (activeRow != -1) + { + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation anot = aa[activeRow]; + + if (anot.description.equals("secondary structure")) + { + // System.out.println(anot.description+" "+anot.getRNAStruc()); + } + } } - //TODO mouseClicked-content and drawCursor are quite experimental! - public void drawCursor(Graphics graphics, 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); + // TODO mouseClicked-content and drawCursor are quite experimental! + public void drawCursor(Graphics graphics, 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); - char s = seq.getCharAt(res); + if (av.validCharWidth) + { + graphics.setColor(Color.white); - charOffset = (av.charWidth - fm.charWidth(s)) / 2; - graphics.drawString(String.valueOf(s), charOffset + x1, - (y1 + av.charHeight) - pady); - } + char s = seq.getCharAt(res); - } + charOffset = (av.charWidth - fm.charWidth(s)) / 2; + graphics.drawString(String.valueOf(s), charOffset + x1, + (y1 + av.charHeight) - pady); + } + + } /** * DOCUMENT ME! @@ -871,7 +880,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, boolean[] graphGroupDrawn = new boolean[aa.length]; int charOffset = 0; // offset for a label float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a - // column. + // column. Font ofont = g.getFont(); // \u03B2 \u03B1 for (int i = 0; i < aa.length; i++) @@ -1058,17 +1067,16 @@ public class AnnotationPanel extends JPanel implements MouseListener, } if (row.hasIcons) { - char ss=row.annotations[column].secondaryStructure; - if (ss=='S') + char ss = row.annotations[column].secondaryStructure; + if (ss == 'S') { // distinguish between forward/backward base-pairing - if (row.annotations[column].displayCharacter.indexOf(')')>-1) + if (row.annotations[column].displayCharacter.indexOf(')') > -1) { - ss='s'; + ss = 's'; } } - if (!validRes - || (ss != lastSS)) + if (!validRes || (ss != lastSS)) { if (x > -1) { @@ -1228,18 +1236,18 @@ public class AnnotationPanel extends JPanel implements MouseListener, int x1 = lastSSX; int x2 = (x * av.charWidth); Regex closeparen = new Regex("(\\))"); - - String dc = column==0 ? "" : row.annotations[column - 1].displayCharacter; - - boolean diffupstream=sCol == 0 || row.annotations[sCol - 1] == null + + String dc = column == 0 ? "" + : row.annotations[column - 1].displayCharacter; + + boolean diffupstream = sCol == 0 || row.annotations[sCol - 1] == null || !dc.equals(row.annotations[sCol - 1].displayCharacter); - boolean diffdownstream=!validRes || !validEnd || row.annotations[column] == null + boolean diffdownstream = !validRes || !validEnd + || row.annotations[column] == null || !dc.equals(row.annotations[column].displayCharacter); - //System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream); + // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream); // If a closing base pair half of the stem, display a backward arrow - if (column > 0 - && closeparen - .search(dc)) + if (column > 0 && closeparen.search(dc)) { if (diffupstream) // if (validRes && column>1 && row.annotations[column-2]!=null && @@ -1252,7 +1260,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, } if (diffdownstream) { - x2-=1; + x2 -= 1; } } else @@ -1267,7 +1275,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, } if (diffupstream) { - x1+=1; + x1 += 1; } } // draw arrow body @@ -1279,7 +1287,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, int column, boolean validRes, boolean validEnd) { g.setColor(Color.gray); - g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) - lastSSX, 2); + g + .fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) + - lastSSX, 2); } private void drawSheetAnnot(Graphics g, AlignmentAnnotation row, @@ -1320,27 +1330,33 @@ public class AnnotationPanel extends JPanel implements MouseListener, if (MAC) { - int ofs=av.charWidth/2; + int ofs = av.charWidth / 2; // Off by 1 offset when drawing rects and ovals // to offscreen image on the MAC - g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2-x1, 8, 8, 8); + g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8); if (sCol == 0 || row.annotations[sCol - 1] == null || row.annotations[sCol - 1].secondaryStructure != 'H') { - } else { -// g.setColor(Color.orange); - g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2-x1-ofs+1, 8, 0, 0); } - if (!validRes || row.annotations[column] == null + else + { + // g.setColor(Color.orange); + g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8, + 0, 0); + } + if (!validRes || row.annotations[column] == null || row.annotations[column].secondaryStructure != 'H') { - - } else { -// g.setColor(Color.magenta); - g.fillRoundRect(lastSSX+ofs, y + 4 + iconOffset, x2-x1-ofs+1, 8, 0, 0); - + + } + else + { + // g.setColor(Color.magenta); + g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs + + 1, 8, 0, 0); + } - + return; } @@ -1351,7 +1367,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, x1 += av.charWidth / 2; } - if (!validRes || row.annotations[column] == null + if (!validRes || row.annotations[column] == null || row.annotations[column].secondaryStructure != 'H') { g.fillArc((x * av.charWidth) - av.charWidth, y + 4 + iconOffset, @@ -1362,7 +1378,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); } -public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, + public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, int eRes, int y, float min, float max, int graphHeight) { if (sRes > aa.annotations.length) @@ -1536,53 +1552,85 @@ public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, // draw profile if available if (renderProfile && aa.annotations[column].value != 0) { + int profl[] = getProfileFor(aa, column); - /*if(profl != null){ - for(int i=0; i 2) + /* + * if (profl != null) { + * + * for (int i = 0; i < profl.length; i++) { System.out.print(profl[i] + * + ","); } + * + * } + */ + int ht = y1, htn = y2 - y1;// aa.graphHeight; + float wdth; + double ht2 = 0; + char[] dc; + + /** + * profl.length == 11 indicates that the profile of a secondary + * structure conservation row was accesed. + * Therefore dc gets length 2, to have space for a basepair instead of + * just a single nucleotide + */ + if (profl.length == 22) { - ht += (int) ht2; + dc = new char[2]; } + else { - // if (aa.annotations[column].value==0) { - // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, - // (ht2=(aa.graphHeight*0.1/av.charHeight))))); - // ht = y2-(int)ht2; - // } else { - g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance( - wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0)) - / av.charHeight))); - lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g); - // htn -=ht2; - // } - g.setColor(profcolour.findColour(dc[0])); // (av.globalColourScheme!=null) - // ? );// try to get a - // colourscheme for the - // group(aa.groupRef.cs==null) - // ? av.textColour2 : - // cs.findColour(dc)); - //System.out.println(dc[0]); - g.drawChars(dc, 0, 1, x * av.charWidth, - (int) (ht + lm.getHeight())); - // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent(); + dc = new char[1]; + } + + LineMetrics lm; + for (int c = 1; profl != null && c < profl[0];) + { + dc[0] = (char) profl[c++]; + + if (aa.label.startsWith("StrucConsensus")) + { + dc[1] = 'A'; + } + + wdth = av.charWidth; + wdth /= (float) fm.charsWidth(dc, 0, dc.length); + + if (c > 2) + { + ht += (int) ht2; + } + { + // if (aa.annotations[column].value==0) { + // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, + // (ht2=(aa.graphHeight*0.1/av.charHeight))))); + // ht = y2-(int)ht2; + // } else { + g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance( + wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0)) + / av.charHeight))); + lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g); + // htn -=ht2; + // } + g.setColor(profcolour.findColour(dc[0])); // (av.globalColourScheme!=null) + // ? );// try to get a + // colourscheme for the + // group(aa.groupRef.cs==null) + // ? av.textColour2 : + // cs.findColour(dc)); + // System.out.println(dc[0]); + + g.drawChars(dc, 0, dc.length, x * av.charWidth, + (int) (ht + lm.getHeight())); + + // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent(); + } } + g.setFont(ofont); } - g.setFont(ofont); } x++; } @@ -1608,35 +1656,40 @@ public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, && aa.groupRef.isShowSequenceLogo()) { return AAFrequency.extractProfile( - aa.groupRef.consensusData[column], - aa.groupRef.getIgnoreGapsConsensus()); + aa.groupRef.consensusData[column], aa.groupRef + .getIgnoreGapsConsensus()); } // TODO extend annotation row to enable dynamic and static profile data to // be stored if (aa.groupRef == null && aa.sequenceRef == null && av.isShowSequenceLogo()) { - return AAFrequency.extractProfile(av.hconsensus[column], - av.getIgnoreGapsConsensus()); + return AAFrequency.extractProfile(av.hconsensus[column], av + .getIgnoreGapsConsensus()); } - }else{ - if (aa.autoCalculated && aa.label.startsWith("StrucConsensus")){ - if (aa.groupRef != null && aa.groupRef.consensusData != null - && aa.groupRef.isShowSequenceLogo()) - { - return StructureFrequency.extractProfile( - aa.groupRef.consensusData[column], - aa.groupRef.getIgnoreGapsConsensus()); - } - // TODO extend annotation row to enable dynamic and static profile data to - // be stored - if (aa.groupRef == null && aa.sequenceRef == null - && av.isShowSequenceLogo()) - { - return StructureFrequency.extractProfile(av.hconsensus[column], - av.getIgnoreGapsConsensus()); - } + } + else + { + if (aa.autoCalculated && aa.label.startsWith("StrucConsensus")) + { + if (aa.groupRef != null && aa.groupRef.consensusData != null + && aa.groupRef.isShowSequenceLogo()) + { + //TODO check what happens for group selections + return StructureFrequency.extractProfile( + aa.groupRef.consensusData[column], aa.groupRef + .getIgnoreGapsConsensus(),column); } + // TODO extend annotation row to enable dynamic and static profile data + // to + // be stored + if (aa.groupRef == null && aa.sequenceRef == null + && av.isShowSequenceLogo()) + { + return StructureFrequency.extractProfile(av.hStrucConsensus[column], + av.getIgnoreGapsConsensus(),column); + } + } } return null; -- 1.7.10.2