/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * \r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
* as published by the Free Software Foundation; either version 2\r
* of the License, or (at your option) any later version.\r
- *\r
+ * \r
* This program is distributed in the hope that it will be useful,\r
* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
* GNU General Public License for more details.\r
- *\r
+ * \r
* You should have received a copy of the GNU General Public License\r
* along with this program; if not, write to the Free Software\r
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
*/\r
-\r
package jalview.io;\r
\r
import java.io.*;\r
-import jalview.datamodel.*;\r
+import java.net.*;\r
import java.util.*;\r
-import java.net.URL;\r
-import jalview.schemes.*;\r
\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
\r
public class AnnotationFile\r
{\r
-\r
- public String printAnnotations(AlignmentAnnotation [] annotations)\r
+ StringBuffer text = new StringBuffer("JALVIEW_ANNOTATION\n"\r
+ + "# Created: " + new java.util.Date() + "\n\n");\r
+\r
+ /**\r
+ * convenience method for pre-2.4 feature files which have no view, hidden\r
+ * columns or hidden row keywords.\r
+ * \r
+ * @param annotations\r
+ * @param groups\r
+ * @param properties\r
+ * @return feature file as a string.\r
+ */\r
+ public String printAnnotations(AlignmentAnnotation[] annotations,\r
+ Vector groups, Hashtable properties)\r
{\r
- StringBuffer text = new StringBuffer(\r
- "JALVIEW_ANNOTATION\n"\r
- +"# Created: "\r
- +new java.util.Date()+"\n\n");\r
+ return printAnnotations(annotations, groups, properties, null);\r
\r
- AlignmentAnnotation row;\r
- String comma;\r
- SequenceI seqref = null;\r
+ }\r
\r
- StringBuffer colours = new StringBuffer();\r
- StringBuffer graphLine = new StringBuffer();\r
+ /**\r
+ * hold all the information about a particular view definition read from or\r
+ * written out in an annotations file.\r
+ */\r
+ public class ViewDef\r
+ {\r
+ public String viewname;\r
\r
- Hashtable graphGroup = new Hashtable();\r
+ public HiddenSequences hidseqs;\r
\r
- java.awt.Color color;\r
+ public ColumnSelection hiddencols;\r
\r
- for(int i=0; i<annotations.length; i++)\r
+ public Vector visibleGroups;\r
+ public Hashtable hiddenRepSeqs;\r
+ \r
+ public ViewDef(String viewname, HiddenSequences hidseqs,\r
+ ColumnSelection hiddencols, Hashtable hiddenRepSeqs)\r
{\r
- row = annotations[i];\r
+ this.viewname = viewname;\r
+ this.hidseqs = hidseqs;\r
+ this.hiddencols = hiddencols;\r
+ this.hiddenRepSeqs = hiddenRepSeqs;\r
+ }\r
+ }\r
\r
- if(!row.visible)\r
- continue;\r
+ public String printAnnotations(AlignmentAnnotation[] annotations,\r
+ Vector groups, Hashtable properties, ViewDef[] views)\r
+ {\r
+ if (annotations != null)\r
+ {\r
+ boolean oneColour = true;\r
+ AlignmentAnnotation row;\r
+ String comma;\r
+ SequenceI refSeq = null;\r
\r
- color = null;\r
+ StringBuffer colours = new StringBuffer();\r
+ StringBuffer graphLine = new StringBuffer();\r
\r
- if( row.sequenceRef == null)\r
- {\r
- if(seqref!=null)\r
- text.append("\nSEQUENCE_REF\tALIGNMENT\n");\r
+ Hashtable graphGroup = new Hashtable();\r
\r
- seqref = null;\r
- }\r
+ java.awt.Color color;\r
\r
- else if (seqref == null || seqref != row.sequenceRef)\r
+ for (int i = 0; i < annotations.length; i++)\r
{\r
- seqref = row.sequenceRef;\r
- text.append("\nSEQUENCE_REF\t" + seqref.getName() + "\n");\r
- }\r
+ row = annotations[i];\r
\r
+ if (!row.visible && !row.hasScore())\r
+ {\r
+ continue;\r
+ }\r
\r
- if( row.graph == AlignmentAnnotation.NO_GRAPH)\r
- {\r
+ color = null;\r
+ oneColour = true;\r
+\r
+ if (row.sequenceRef == null)\r
+ {\r
+ if (refSeq != null)\r
+ {\r
+ text.append("\nSEQUENCE_REF\tALIGNMENT\n");\r
+ }\r
+\r
+ refSeq = null;\r
+ }\r
+\r
+ else if (refSeq == null || refSeq != row.sequenceRef)\r
+ {\r
+ refSeq = row.sequenceRef;\r
+ text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");\r
+ }\r
+\r
+ if (row.graph == AlignmentAnnotation.NO_GRAPH)\r
+ {\r
text.append("NO_GRAPH\t");\r
- }\r
- else\r
- {\r
- if( row.graph == AlignmentAnnotation.BAR_GRAPH)\r
- text.append("BAR_GRAPH\t");\r
- else if(row.graph == AlignmentAnnotation.LINE_GRAPH)\r
- text.append("LINE_GRAPH\t");\r
-\r
- if(row.getThreshold()!=null)\r
- graphLine.append("GRAPHLINE\t"\r
- + row.label + "\t"\r
- + row.getThreshold().value + "\t"\r
- + row.getThreshold().label + "\t"\r
- + jalview.util.Format.getHexString(\r
- row.getThreshold().colour)+"\n"\r
- );\r
-\r
- if(row.graphGroup>-1)\r
+ }\r
+ else\r
+ {\r
+ if (row.graph == AlignmentAnnotation.BAR_GRAPH)\r
+ {\r
+ text.append("BAR_GRAPH\t");\r
+ }\r
+ else if (row.graph == AlignmentAnnotation.LINE_GRAPH)\r
+ {\r
+ text.append("LINE_GRAPH\t");\r
+ }\r
+\r
+ if (row.getThreshold() != null)\r
+ {\r
+ graphLine\r
+ .append("GRAPHLINE\t"\r
+ + row.label\r
+ + "\t"\r
+ + row.getThreshold().value\r
+ + "\t"\r
+ + row.getThreshold().label\r
+ + "\t"\r
+ + jalview.util.Format.getHexString(row\r
+ .getThreshold().colour) + "\n");\r
+ }\r
+\r
+ if (row.graphGroup > -1)\r
{\r
String key = String.valueOf(row.graphGroup);\r
- if(graphGroup.containsKey(key))\r
- graphGroup.put(key, graphGroup.get(key)\r
- +"\t"+row.label);\r
+ if (graphGroup.containsKey(key))\r
+ {\r
+ graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);\r
+ }\r
else\r
+ {\r
graphGroup.put(key, row.label);\r
+ }\r
}\r
- }\r
-\r
- text.append(row.label+"\t");\r
- if(row.description!=null)\r
- text.append(row.description+"\t");\r
+ }\r
\r
- for(int j=0; j<row.annotations.length; j++)\r
- {\r
- if (seqref != null && jalview.util.Comparison.isGap(seqref.getCharAt(j)))\r
- continue;\r
+ text.append(row.label + "\t");\r
+ if (row.description != null)\r
+ {\r
+ text.append(row.description + "\t");\r
+ }\r
\r
- if(row.annotations[j]!=null)\r
+ for (int j = 0; row.annotations != null\r
+ && j < row.annotations.length; j++)\r
{\r
- comma = "";\r
- if (row.annotations[j].secondaryStructure!=' ')\r
+ if (refSeq != null\r
+ && jalview.util.Comparison.isGap(refSeq.getCharAt(j)))\r
{\r
- text.append(comma + row.annotations[j].secondaryStructure);\r
- comma = ",";\r
+ continue;\r
}\r
- if (row.annotations[j].displayCharacter.length() > 0\r
- && !row.annotations[j].displayCharacter.equals(" "))\r
+\r
+ if (row.annotations[j] != null)\r
+ {\r
+ comma = "";\r
+ if (row.annotations[j].secondaryStructure != ' ')\r
+ {\r
+ text.append(comma + row.annotations[j].secondaryStructure);\r
+ comma = ",";\r
+ }\r
+ if (row.annotations[j].displayCharacter != null\r
+ && row.annotations[j].displayCharacter.length() > 0\r
+ && !row.annotations[j].displayCharacter.equals(" "))\r
+ {\r
+ text.append(comma + row.annotations[j].displayCharacter);\r
+ comma = ",";\r
+ }\r
+\r
+ if (row.annotations[j] != null)\r
+ {\r
+ if (color != null && !color.equals(row.annotations[j].colour))\r
{\r
- text.append(comma + row.annotations[j].displayCharacter);\r
- comma = ",";\r
+ oneColour = false;\r
}\r
\r
- if (row.annotations[j]!=null)\r
- {\r
- color = row.annotations[j].colour;\r
- if (row.annotations[j].value!=0f)\r
- text.append(comma + row.annotations[j].value);\r
+ color = row.annotations[j].colour;\r
+ if (row.annotations[j].value != 0f\r
+ && row.annotations[j].value != Float.NaN)\r
+ {\r
+ text.append(comma + row.annotations[j].value);\r
+ }\r
+ }\r
+\r
+ if (row.annotations[j].colour != null\r
+ && row.annotations[j].colour != java.awt.Color.black)\r
+ {\r
+ text.append(comma\r
+ + "["\r
+ + jalview.util.Format\r
+ .getHexString(row.annotations[j].colour)\r
+ + "]");\r
+ }\r
}\r
+ text.append("|");\r
}\r
- text.append("|");\r
+\r
+ if (row.hasScore())\r
+ text.append("\t" + row.score);\r
+\r
+ text.append("\n");\r
+\r
+ if (color != null && color != java.awt.Color.black && oneColour)\r
+ {\r
+ colours.append("COLOUR\t" + row.label + "\t"\r
+ + jalview.util.Format.getHexString(color) + "\n");\r
+ }\r
+\r
}\r
\r
text.append("\n");\r
\r
- if(color!=null && color!=java.awt.Color.black)\r
+ text.append(colours.toString());\r
+ text.append(graphLine.toString());\r
+ if (graphGroup.size() > 0)\r
{\r
- colours.append("COLOUR\t"\r
- +row.label+"\t"\r
- +jalview.util.Format.getHexString(color)+"\n");\r
+ text.append("COMBINE\t");\r
+ Enumeration en = graphGroup.elements();\r
+ while (en.hasMoreElements())\r
+ {\r
+ text.append(en.nextElement() + "\n");\r
+ }\r
}\r
-\r
}\r
\r
- text.append("\n");\r
+ if (groups != null)\r
+ {\r
+ printGroups(groups);\r
+ }\r
\r
- text.append(colours.toString());\r
- text.append(graphLine.toString());\r
- if(graphGroup.size()>0)\r
+ if (properties != null)\r
{\r
- text.append("COMBINE\t");\r
- Enumeration en = graphGroup.elements();\r
- while(en.hasMoreElements())\r
+ text.append("\n\nALIGNMENT");\r
+ Enumeration en = properties.keys();\r
+ while (en.hasMoreElements())\r
{\r
- text.append(en.nextElement()+"\n");\r
+ String key = en.nextElement().toString();\r
+ text.append("\t" + key + "=" + properties.get(key));\r
}\r
+ // TODO: output alignment visualization settings here if required\r
+\r
}\r
\r
return text.toString();\r
}\r
\r
+ public void printGroups(Vector sequenceGroups)\r
+ {\r
+ SequenceGroup sg;\r
+ SequenceI seqrep=null;\r
+ for (int i = 0; i < sequenceGroups.size(); i++)\r
+ {\r
+ sg = (SequenceGroup) sequenceGroups.elementAt(i);\r
+ if (!sg.hasSeqrep())\r
+ {\r
+ text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"\r
+ + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1) + "\t"\r
+ + "-1\t");\r
+ seqrep = null;\r
+ } else {\r
+ seqrep = sg.getSeqrep();\r
+ text.append("SEQUENCE_REF\t"+seqrep.getName()+"\n");\r
+ text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"\r
+ + (seqrep.findPosition(sg.getStartRes())) + "\t" + (seqrep.findPosition(sg.getEndRes())) + "\t"\r
+ + "-1\t");\r
+ }\r
+ for (int s = 0; s < sg.getSize(); s++)\r
+ {\r
+ text.append(sg.getSequenceAt(s).getName() + "\t");\r
+ }\r
+\r
+ text.append("\nPROPERTIES\t" + sg.getName() + "\t");\r
+\r
+ if (sg.getDescription() != null)\r
+ {\r
+ text.append("description=" + sg.getDescription() + "\t");\r
+ }\r
+ if (sg.cs != null)\r
+ {\r
+ text.append("colour=" + ColourSchemeProperty.getColourName(sg.cs)\r
+ + "\t");\r
+ if (sg.cs.getThreshold() != 0)\r
+ {\r
+ text.append("pidThreshold=" + sg.cs.getThreshold());\r
+ }\r
+ if (sg.cs.conservationApplied())\r
+ {\r
+ text.append("consThreshold=" + sg.cs.getConservationInc() + "\t");\r
+ }\r
+ }\r
+ text.append("outlineColour="\r
+ + jalview.util.Format.getHexString(sg.getOutlineColour())\r
+ + "\t");\r
+\r
+ text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");\r
+ text.append("displayText=" + sg.getDisplayText() + "\t");\r
+ text.append("colourText=" + sg.getColourText() + "\t");\r
+ text.append("showUnconserved="+sg.getShowunconserved()+"\t");\r
+ if (sg.textColour != java.awt.Color.black)\r
+ {\r
+ text.append("textCol1="\r
+ + jalview.util.Format.getHexString(sg.textColour) + "\t");\r
+ }\r
+ if (sg.textColour2 != java.awt.Color.white)\r
+ {\r
+ text.append("textCol2="\r
+ + jalview.util.Format.getHexString(sg.textColour2) + "\t");\r
+ }\r
+ if (sg.thresholdTextColour != 0)\r
+ {\r
+ text.append("textColThreshold=" + sg.thresholdTextColour+"\t");\r
+ }\r
+ if (sg.idColour != null)\r
+ {\r
+ text.append("idColour="\r
+ + jalview.util.Format.getHexString(sg.idColour) + "\t");\r
+ }\r
+ if (sg.isHidereps())\r
+ {\r
+ text.append("hide=true\t");\r
+ }\r
+ if (sg.isHideCols())\r
+ {\r
+ text.append("hidecols=true\t");\r
+ }\r
+ if (seqrep!=null)\r
+ {\r
+ // terminate the last line and clear the sequence ref for the group\r
+ text.append("\nSEQUENCE_REF");\r
+ }\r
+ text.append("\n\n");\r
+\r
+ }\r
+ }\r
\r
SequenceI refSeq = null;\r
- Hashtable annotationsHash = new Hashtable();\r
- public boolean readAnnotationFile(AlignmentI al,\r
- String file,\r
- String protocol)\r
+\r
+ String refSeqId = null;\r
+\r
+ public boolean readAnnotationFile(AlignmentI al, String file,\r
+ String protocol)\r
{\r
try\r
{\r
URL url = new URL(file);\r
in = new BufferedReader(new InputStreamReader(url.openStream()));\r
}\r
- else if (protocol.equals(AppletFormatAdapter.PASTE))\r
+ else if (protocol.equals(AppletFormatAdapter.PASTE))\r
{\r
in = new BufferedReader(new StringReader(file));\r
}\r
{\r
in = new BufferedReader(new java.io.InputStreamReader(is));\r
}\r
- }\r
+ }\r
\r
String line, label, description, token;\r
int graphStyle, index;\r
int refSeqIndex = 1;\r
int existingAnnotations = 0;\r
- if(al.getAlignmentAnnotation()!=null)\r
- existingAnnotations = al.getAlignmentAnnotation().length;\r
+ if (al.getAlignmentAnnotation() != null)\r
+ {\r
+ existingAnnotations = al.getAlignmentAnnotation().length;\r
+ }\r
\r
int alWidth = al.getWidth();\r
\r
\r
// First confirm this is an Annotation file\r
boolean jvAnnotationFile = false;\r
- while ( (line = in.readLine()) != null)\r
+ while ((line = in.readLine()) != null)\r
{\r
- if (line.indexOf("#") == 0 )\r
+ if (line.indexOf("#") == 0)\r
+ {\r
continue;\r
+ }\r
\r
if (line.indexOf("JALVIEW_ANNOTATION") > -1)\r
{\r
}\r
}\r
\r
- if(!jvAnnotationFile)\r
+ if (!jvAnnotationFile)\r
{\r
in.close();\r
return false;\r
}\r
\r
- while ( (line = in.readLine()) != null)\r
+ while ((line = in.readLine()) != null)\r
{\r
- if(line.indexOf("#")==0\r
- || line.indexOf("JALVIEW_ANNOTATION")>-1\r
- || line.length()==0)\r
+ if (line.indexOf("#") == 0\r
+ || line.indexOf("JALVIEW_ANNOTATION") > -1\r
+ || line.length() == 0)\r
+ {\r
continue;\r
+ }\r
\r
st = new StringTokenizer(line, "\t");\r
token = st.nextToken();\r
- if(token.equalsIgnoreCase("COLOUR"))\r
+ if (token.equalsIgnoreCase("COLOUR"))\r
{\r
+ // TODO: use graduated colour def'n here too\r
colourAnnotations(al, st.nextToken(), st.nextToken());\r
continue;\r
}\r
\r
- else if(token.equalsIgnoreCase("COMBINE") )\r
+ else if (token.equalsIgnoreCase("COMBINE"))\r
{\r
combineAnnotations(al, st);\r
continue;\r
continue;\r
}\r
\r
-\r
- else if(token.equalsIgnoreCase("SEQUENCE_REF") )\r
+ else if (token.equalsIgnoreCase("SEQUENCE_REF"))\r
{\r
- refSeq = al.findName(st.nextToken());\r
- try{\r
- refSeqIndex = Integer.parseInt(st.nextToken());\r
- if(refSeqIndex<1)\r
+ if (st.hasMoreTokens())\r
+ {\r
+ refSeq = al.findName(refSeqId = st.nextToken());\r
+ if (refSeq == null)\r
+ {\r
+ refSeqId = null;\r
+ }\r
+ try\r
+ {\r
+ refSeqIndex = Integer.parseInt(st.nextToken());\r
+ if (refSeqIndex < 1)\r
+ {\r
+ refSeqIndex = 1;\r
+ System.out\r
+ .println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");\r
+ }\r
+ } catch (Exception ex)\r
{\r
refSeqIndex = 1;\r
- System.out.println("WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");\r
}\r
}\r
- catch(Exception ex)\r
+ else\r
{\r
- refSeqIndex = 1;\r
+ refSeq = null;\r
+ refSeqId = null;\r
}\r
-\r
continue;\r
}\r
\r
- else if(token.equalsIgnoreCase("SEQUENCE_GROUP"))\r
+ else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))\r
{\r
addGroup(al, st);\r
continue;\r
}\r
\r
- else if(token.equalsIgnoreCase("PROPERTIES"))\r
+ else if (token.equalsIgnoreCase("PROPERTIES"))\r
{\r
addProperties(al, st);\r
continue;\r
}\r
\r
+ else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))\r
+ {\r
+ setBelowAlignment(al, st);\r
+ continue;\r
+ }\r
+ else if (token.equalsIgnoreCase("ALIGNMENT"))\r
+ {\r
+ addAlignmentDetails(al, st);\r
+ continue;\r
+ }\r
\r
graphStyle = AlignmentAnnotation.getGraphValueFromString(token);\r
label = st.nextToken();\r
\r
- if(st.countTokens()>1)\r
- description = st.nextToken();\r
- else\r
- description = null;\r
-\r
- line = st.nextToken();\r
-\r
- st = new StringTokenizer(line, "|", true);\r
- annotations = new Annotation[alWidth];\r
-\r
index = 0;\r
- boolean emptyColumn = true;\r
-\r
+ annotations = new Annotation[alWidth];\r
+ description = null;\r
+ float score = Float.NaN;\r
\r
- while (st.hasMoreElements() && index<alWidth)\r
+ if (st.hasMoreTokens())\r
{\r
- token = st.nextToken().trim();\r
- if(token.equals("|"))\r
+ line = st.nextToken();\r
+\r
+ if (line.indexOf("|") == -1)\r
{\r
- if(emptyColumn)\r
- index++;\r
+ description = line;\r
+ if (st.hasMoreTokens())\r
+ line = st.nextToken();\r
+ }\r
\r
- emptyColumn = true;\r
+ if (st.hasMoreTokens())\r
+ {\r
+ // This must be the score\r
+ score = Float.valueOf(st.nextToken()).floatValue();\r
}\r
- else\r
+\r
+ st = new StringTokenizer(line, "|", true);\r
+\r
+ boolean emptyColumn = true;\r
+ boolean onlyOneElement = (st.countTokens() == 1);\r
+\r
+ while (st.hasMoreElements() && index < alWidth)\r
{\r
- annotations[index++] = parseAnnotation(token);\r
- emptyColumn = false;\r
+ token = st.nextToken().trim();\r
+\r
+ if (onlyOneElement)\r
+ {\r
+ try\r
+ {\r
+ score = Float.valueOf(token).floatValue();\r
+ break;\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ }\r
+ }\r
+\r
+ if (token.equals("|"))\r
+ {\r
+ if (emptyColumn)\r
+ {\r
+ index++;\r
+ }\r
+\r
+ emptyColumn = true;\r
+ }\r
+ else\r
+ {\r
+ annotations[index++] = parseAnnotation(token);\r
+ emptyColumn = false;\r
+ }\r
}\r
- }\r
\r
- annotation = new AlignmentAnnotation(label,\r
- description,\r
- annotations,\r
- 0,\r
- 0,\r
- graphStyle);\r
+ }\r
\r
- if(refSeq!=null)\r
- {\r
- annotation.createSequenceMapping(refSeq, refSeqIndex, false);\r
- refSeq.addAlignmentAnnotation(annotation);\r
- }\r
+ annotation = new AlignmentAnnotation(label, description,\r
+ (index == 0) ? null : annotations, 0, 0, graphStyle);\r
\r
- al.addAnnotation(annotation);\r
+ annotation.score = score;\r
\r
- al.setAnnotationIndex(annotation, al.getAlignmentAnnotation().length - existingAnnotations-1);\r
+ if (refSeq != null)\r
+ {\r
+ annotation.belowAlignment = false;\r
+ // make a copy of refSeq so we can find other matches in the alignment\r
+ SequenceI referedSeq = refSeq;\r
+ do\r
+ {\r
+ // copy before we do any mapping business.\r
+ // TODO: verify that undo/redo with 1:many sequence associated\r
+ // annotations can be undone correctly\r
+ AlignmentAnnotation ann = new AlignmentAnnotation(annotation);\r
+ annotation.createSequenceMapping(referedSeq, refSeqIndex, false);\r
+ annotation.adjustForAlignment();\r
+ referedSeq.addAlignmentAnnotation(annotation);\r
+ al.addAnnotation(annotation);\r
+ al.setAnnotationIndex(annotation,\r
+ al.getAlignmentAnnotation().length\r
+ - existingAnnotations - 1);\r
+ // and recover our virgin copy to use again if necessary.\r
+ annotation = ann;\r
+\r
+ } while (refSeqId != null\r
+ && (referedSeq = al.findName(referedSeq, refSeqId, true)) != null);\r
+ }\r
+ else\r
+ {\r
+ al.addAnnotation(annotation);\r
+ al.setAnnotationIndex(annotation,\r
+ al.getAlignmentAnnotation().length - existingAnnotations\r
+ - 1);\r
+ }\r
}\r
\r
- }catch(Exception ex)\r
+ } catch (Exception ex)\r
{\r
ex.printStackTrace();\r
- System.out.println("Problem reading annotation file: "+ex);\r
+ System.out.println("Problem reading annotation file: " + ex);\r
return false;\r
}\r
return true;\r
\r
Annotation parseAnnotation(String string)\r
{\r
- String desc = null, displayChar="";\r
+ String desc = null, displayChar = null;\r
char ss = ' '; // secondaryStructure\r
float value = 0;\r
boolean parsedValue = false;\r
+\r
+ // find colour here\r
+ java.awt.Color colour = null;\r
+ int i = string.indexOf("[");\r
+ int j = string.indexOf("]");\r
+ if (i > -1 && j > -1)\r
+ {\r
+ UserColourScheme ucs = new UserColourScheme();\r
+\r
+ colour = ucs.getColourFromString(string.substring(i + 1, j));\r
+\r
+ string = string.substring(0, i) + string.substring(j + 1);\r
+ }\r
+\r
StringTokenizer st = new StringTokenizer(string, ",");\r
String token;\r
- while(st.hasMoreTokens())\r
+ while (st.hasMoreTokens())\r
{\r
token = st.nextToken().trim();\r
- if(token.length()==0)\r
+ if (token.length() == 0)\r
+ {\r
continue;\r
+ }\r
\r
- if(!parsedValue)\r
+ if (!parsedValue)\r
{\r
- try{\r
+ try\r
+ {\r
displayChar = token;\r
value = new Float(token).floatValue();\r
parsedValue = true;\r
continue;\r
- }catch(NumberFormatException ex){}\r
+ } catch (NumberFormatException ex)\r
+ {\r
+ }\r
}\r
\r
- if(token.equals("H") || token.equals("E"))\r
+ if (token.equals("H") || token.equals("E"))\r
{\r
// Either this character represents a helix or sheet\r
// or an integer which can be displayed\r
ss = token.charAt(0);\r
- if(displayChar.equals(token.substring(0,1)))\r
+ if (displayChar.equals(token.substring(0, 1)))\r
+ {\r
displayChar = "";\r
+ }\r
}\r
- else if(desc==null)\r
+ else if (desc == null)\r
+ {\r
desc = token;\r
+ }\r
\r
}\r
\r
- if(desc == null)\r
- desc = value+"";\r
-\r
- if(displayChar.length()>1 && desc.length()==1)\r
+ if (displayChar != null && displayChar.length() > 1 && desc != null\r
+ && desc.length() == 1)\r
{\r
String tmp = displayChar;\r
displayChar = desc;\r
desc = tmp;\r
}\r
+ /*\r
+ * In principle, this code will ensure that the Annotation element generated\r
+ * is renderable by any of the applet or application rendering code but\r
+ * instead we check for null strings when the display character is rendered.\r
+ * if (displayChar==null) { displayChar=""; }\r
+ */\r
+ Annotation anot = new Annotation(displayChar, desc, ss, value);\r
+\r
+ anot.colour = colour;\r
\r
- return new Annotation(displayChar, desc, ss, value);\r
+ return anot;\r
}\r
\r
void colourAnnotations(AlignmentI al, String label, String colour)\r
{\r
UserColourScheme ucs = new UserColourScheme(colour);\r
Annotation[] annotations;\r
- for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
+ for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
{\r
- if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))\r
+ if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(label))\r
{\r
annotations = al.getAlignmentAnnotation()[i].annotations;\r
- for(int j=0; j<annotations.length; j++)\r
+ for (int j = 0; j < annotations.length; j++)\r
{\r
- if(annotations[j]!=null)\r
+ if (annotations[j] != null)\r
+ {\r
annotations[j].colour = ucs.findColour('A');\r
+ }\r
}\r
}\r
}\r
{\r
int graphGroup = -1;\r
String group = st.nextToken();\r
- //First make sure we are not overwriting the graphIndex\r
- for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
+ // First make sure we are not overwriting the graphIndex\r
+ for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
{\r
- if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
+ if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
{\r
- graphGroup = al.getAlignmentAnnotation()[i].graphGroup +1;\r
+ graphGroup = al.getAlignmentAnnotation()[i].graphGroup + 1;\r
al.getAlignmentAnnotation()[i].graphGroup = graphGroup;\r
break;\r
}\r
}\r
\r
- //Now update groups\r
- while(st.hasMoreTokens())\r
+ // Now update groups\r
+ while (st.hasMoreTokens())\r
{\r
group = st.nextToken();\r
- for(int i=0; i<al.getAlignmentAnnotation().length; i++)\r
+ for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
{\r
if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
{\r
}\r
}\r
\r
- if(annotation==null)\r
+ if (annotation == null)\r
+ {\r
return;\r
+ }\r
float value = new Float(st.nextToken()).floatValue();\r
- String label = st.hasMoreTokens() ? st.nextToken() : null;\r
+ String label = st.hasMoreTokens() ? st.nextToken() : null;\r
java.awt.Color colour = null;\r
- if(st.hasMoreTokens())\r
+ if (st.hasMoreTokens())\r
{\r
UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
colour = ucs.findColour('A');\r
\r
annotation.setThreshold(new GraphLine(value, label, colour));\r
}\r
-\r
void addGroup(AlignmentI al, StringTokenizer st)\r
{\r
SequenceGroup sg = new SequenceGroup();\r
sg.setName(st.nextToken());\r
- sg.setStartRes(Integer.parseInt(st.nextToken())-1);\r
- sg.setEndRes(Integer.parseInt(st.nextToken())-1);\r
+ String rng ="";\r
+ try {\r
+ rng = st.nextToken();\r
+ if (rng.length()>0 && !rng.startsWith("*"))\r
+ {\r
+ sg.setStartRes(Integer.parseInt(rng) - 1);\r
+ } else {\r
+ sg.setStartRes(0);\r
+ }\r
+ rng = st.nextToken();\r
+ if (rng.length()>0 && !rng.startsWith("*"))\r
+ {\r
+ sg.setEndRes(Integer.parseInt(rng) - 1);\r
+ } else {\r
+ sg.setEndRes(al.getWidth()-1);\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ System.err.println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"+rng+"' - assuming alignment width for group.");\r
+ // assume group is full width\r
+ sg.setStartRes(0);\r
+ sg.setEndRes(al.getWidth()-1);\r
+ }\r
\r
String index = st.nextToken();\r
- if(index.equals("-1"))\r
+ if (index.equals("-1"))\r
{\r
while (st.hasMoreElements())\r
{\r
int end = (Integer.parseInt(st3.nextToken()));\r
\r
if (end > start)\r
+ {\r
for (int i = start; i <= end; i++)\r
- sg.addSequence(al.getSequenceAt(i-1), false);\r
+ {\r
+ sg.addSequence(al.getSequenceAt(i - 1), false);\r
+ }\r
+ }\r
}\r
else\r
{\r
- sg.addSequence(al.getSequenceAt(Integer.parseInt(tmp)-1 ), false);\r
+ sg\r
+ .addSequence(al.getSequenceAt(Integer.parseInt(tmp) - 1),\r
+ false);\r
}\r
}\r
}\r
\r
- if(refSeq!=null)\r
+ if (refSeq != null)\r
{\r
- sg.setStartRes( refSeq.findIndex( sg.getStartRes()+1 )-1 );\r
- sg.setEndRes( refSeq.findIndex( sg.getEndRes() +1) -1 );\r
+ sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);\r
+ sg.setEndRes(refSeq.findIndex(sg.getEndRes() + 1) - 1);\r
+ sg.setSeqrep(refSeq);\r
}\r
\r
-\r
- al.addGroup(sg);\r
- annotationsHash.put(sg.getName(), sg);\r
+ if (sg.getSize() > 0)\r
+ {\r
+ al.addGroup(sg);\r
+ }\r
}\r
\r
void addProperties(AlignmentI al, StringTokenizer st)\r
{\r
\r
- //So far we have only added groups to the annotationHash,\r
- //the idea is in the future properties can be added to\r
- //alignments, other annotations etc\r
- SequenceGroup sg = (SequenceGroup)annotationsHash.get(st.nextToken());\r
+ // So far we have only added groups to the annotationHash,\r
+ // the idea is in the future properties can be added to\r
+ // alignments, other annotations etc\r
+ if (al.getGroups() == null)\r
+ {\r
+ return;\r
+ }\r
+ SequenceGroup sg = null;\r
+\r
+ String name = st.nextToken();\r
+\r
+ Vector groups = al.getGroups();\r
+ for (int i = 0; i < groups.size(); i++)\r
+ {\r
+ sg = (SequenceGroup) groups.elementAt(i);\r
+ if (sg.getName().equals(name))\r
+ {\r
+ break;\r
+ }\r
+ else\r
+ {\r
+ sg = null;\r
+ }\r
+ }\r
\r
- if(sg!=null)\r
+ if (sg != null)\r
{\r
String keyValue, key, value;\r
- while(st.hasMoreTokens())\r
+ ColourSchemeI def = sg.cs;\r
+ sg.cs = null;\r
+ while (st.hasMoreTokens())\r
{\r
keyValue = st.nextToken();\r
- key = keyValue.substring(0,keyValue.indexOf("="));\r
- value=keyValue.substring(keyValue.indexOf("=")+1);\r
+ key = keyValue.substring(0, keyValue.indexOf("="));\r
+ value = keyValue.substring(keyValue.indexOf("=") + 1);\r
\r
- if(key.equalsIgnoreCase("description"))\r
+ if (key.equalsIgnoreCase("description"))\r
+ {\r
sg.setDescription(value);\r
- else if(key.equalsIgnoreCase("colour"))\r
+ }\r
+ else if (key.equalsIgnoreCase("colour"))\r
+ {\r
sg.cs = ColourSchemeProperty.getColour(al, value);\r
+ }\r
else if (key.equalsIgnoreCase("pidThreshold"))\r
- sg.cs.setThreshold(Integer.parseInt(value), false);//\r
- else if (key.equalsIgnoreCase("outlineColour"))\r
- {\r
- sg.setOutlineColour(new UserColourScheme(value).findColour('A'));\r
- }\r
+ {\r
+ sg.cs.setThreshold(Integer.parseInt(value), true);\r
\r
- //Boolean.valueOf(string).booleanValue();\r
+ }\r
+ else if (key.equalsIgnoreCase("consThreshold"))\r
+ {\r
+ sg.cs.setConservationInc(Integer.parseInt(value));\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3, sg.getSequences(null), sg\r
+ .getStartRes(), sg.getEndRes() + 1);\r
+\r
+ c.calculate();\r
+ c.verdict(false, 25);\r
+\r
+ sg.cs.setConservation(c);\r
+\r
+ }\r
+ else if (key.equalsIgnoreCase("outlineColour"))\r
+ {\r
+ sg.setOutlineColour(new UserColourScheme(value).findColour('A'));\r
+ }\r
else if (key.equalsIgnoreCase("displayBoxes"))\r
- sg.setDisplayBoxes( Boolean.valueOf(value).booleanValue() );\r
+ {\r
+ sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());\r
+ }\r
+ else if (key.equalsIgnoreCase("showUnconserved"))\r
+ {\r
+ sg.setShowunconserved(Boolean.valueOf(value).booleanValue());\r
+ }\r
else if (key.equalsIgnoreCase("displayText"))\r
- sg.setDisplayText( Boolean.valueOf(value).booleanValue() );\r
+ {\r
+ sg.setDisplayText(Boolean.valueOf(value).booleanValue());\r
+ }\r
else if (key.equalsIgnoreCase("colourText"))\r
- sg.setColourText( Boolean.valueOf(value).booleanValue() );\r
+ {\r
+ sg.setColourText(Boolean.valueOf(value).booleanValue());\r
+ }\r
else if (key.equalsIgnoreCase("textCol1"))\r
- {\r
- sg.textColour = new UserColourScheme(value).findColour('A');\r
- }\r
+ {\r
+ sg.textColour = new UserColourScheme(value).findColour('A');\r
+ }\r
else if (key.equalsIgnoreCase("textCol2"))\r
{\r
sg.textColour2 = new UserColourScheme(value).findColour('A');\r
}\r
else if (key.equalsIgnoreCase("textColThreshold"))\r
- sg.thresholdTextColour = Integer.parseInt(value);\r
+ {\r
+ sg.thresholdTextColour = Integer.parseInt(value);\r
+ }\r
+ else if (key.equalsIgnoreCase("idColour"))\r
+ {\r
+ // consider warning if colour doesn't resolve to a real colour\r
+ sg.setIdColour((def = new UserColourScheme(value))\r
+ .findColour('A'));\r
+ }\r
+ else if (key.equalsIgnoreCase("hide"))\r
+ {\r
+ // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847\r
+ sg.setHidereps(true);\r
+ }\r
+ else if (key.equalsIgnoreCase("hidecols"))\r
+ {\r
+ // see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=25847\r
+ sg.setHideCols(true);\r
+ }\r
+ sg.recalcConservation();\r
+ }\r
+ if (sg.cs == null)\r
+ {\r
+ sg.cs = def;\r
+ }\r
+ }\r
+ }\r
\r
+ void setBelowAlignment(AlignmentI al, StringTokenizer st)\r
+ {\r
+ String token;\r
+ AlignmentAnnotation aa;\r
+ while (st.hasMoreTokens())\r
+ {\r
+ token = st.nextToken();\r
+ for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
+ {\r
+ aa = al.getAlignmentAnnotation()[i];\r
+ if (aa.sequenceRef == refSeq && aa.label.equals(token))\r
+ {\r
+ aa.belowAlignment = true;\r
+ }\r
}\r
}\r
}\r
+\r
+ void addAlignmentDetails(AlignmentI al, StringTokenizer st)\r
+ {\r
+ String keyValue, key, value;\r
+ while (st.hasMoreTokens())\r
+ {\r
+ keyValue = st.nextToken();\r
+ key = keyValue.substring(0, keyValue.indexOf("="));\r
+ value = keyValue.substring(keyValue.indexOf("=") + 1);\r
+ al.setProperty(key, value);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Write annotations as a CSV file of the form 'label, value, value, ...' for\r
+ * each row.\r
+ * \r
+ * @param annotations\r
+ * @return CSV file as a string.\r
+ */\r
+ public String printCSVAnnotations(AlignmentAnnotation[] annotations)\r
+ {\r
+ StringBuffer sp = new StringBuffer();\r
+ for (int i = 0; i < annotations.length; i++)\r
+ {\r
+ String atos = annotations[i].toString();\r
+ int p = 0;\r
+ do\r
+ {\r
+ int cp = atos.indexOf("\n", p);\r
+ sp.append(annotations[i].label);\r
+ sp.append(",");\r
+ if (cp > p)\r
+ {\r
+ sp.append(atos.substring(p, cp + 1));\r
+ }\r
+ else\r
+ {\r
+ sp.append(atos.substring(p));\r
+ sp.append("\n");\r
+ }\r
+ p = cp + 1;\r
+ } while (p > 0);\r
+ }\r
+ return sp.toString();\r
+ }\r
}\r
git://source.jalview.org / jalview.git / blobdiff