/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 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
\r
public class AnnotationFile\r
{\r
- StringBuffer text = new StringBuffer(\r
- "JALVIEW_ANNOTATION\n"\r
- + "# Created: "\r
- + new java.util.Date() + "\n\n");\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 columns or hidden row keywords.\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,\r
- Hashtable properties)\r
+ Vector groups, Hashtable properties)\r
{\r
- return printAnnotations(annotations, groups,\r
- properties, null);\r
+ return printAnnotations(annotations, groups, properties, null);\r
\r
}\r
+\r
/**\r
- * hold all the information about a particular view definition\r
- * read from or written out in an annotations file.\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
+ public class ViewDef\r
+ {\r
public String viewname;\r
+\r
public HiddenSequences hidseqs;\r
+\r
public ColumnSelection hiddencols;\r
+\r
public Vector visibleGroups;\r
+\r
public ViewDef(String viewname, HiddenSequences hidseqs,\r
ColumnSelection hiddencols)\r
{\r
this.hiddencols = hiddencols;\r
}\r
}\r
+\r
public String printAnnotations(AlignmentAnnotation[] annotations,\r
- Vector groups,\r
- Hashtable properties, ViewDef[] views)\r
+ Vector groups, Hashtable properties, ViewDef[] views)\r
{\r
if (annotations != null)\r
{\r
\r
if (row.getThreshold() != null)\r
{\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
+ 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
String key = String.valueOf(row.graphGroup);\r
if (graphGroup.containsKey(key))\r
{\r
- graphGroup.put(key, graphGroup.get(key)\r
- + "\t" + row.label);\r
+ graphGroup.put(key, graphGroup.get(key) + "\t" + row.label);\r
}\r
else\r
{\r
text.append(row.description + "\t");\r
}\r
\r
- for (int j = 0; row.annotations!=null && j < row.annotations.length; j++)\r
+ for (int j = 0; row.annotations != null\r
+ && j < row.annotations.length; j++)\r
{\r
- if (refSeq != null &&\r
- jalview.util.Comparison.isGap(refSeq.getCharAt(j)))\r
+ if (refSeq != null\r
+ && jalview.util.Comparison.isGap(refSeq.getCharAt(j)))\r
{\r
continue;\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
+ 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
if (row.annotations[j] != null)\r
{\r
- if(color!=null && !color.equals(row.annotations[j].colour))\r
+ if (color != null && !color.equals(row.annotations[j].colour))\r
{\r
oneColour = false;\r
}\r
\r
color = row.annotations[j].colour;\r
- if (row.annotations[j].value != 0f && row.annotations[j].value!=Float.NaN) \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
+ if (row.annotations[j].colour != null\r
+ && row.annotations[j].colour != java.awt.Color.black)\r
{\r
- text.append(comma+"["+\r
- jalview.util.Format.getHexString(\r
- row.annotations[j].colour)+"]");\r
+ text.append(comma\r
+ + "["\r
+ + jalview.util.Format\r
+ .getHexString(row.annotations[j].colour)\r
+ + "]");\r
}\r
}\r
text.append("|");\r
}\r
\r
- if(row.hasScore())\r
- text.append("\t"+row.score);\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"\r
- + row.label + "\t"\r
- + jalview.util.Format.getHexString(color) + "\n");\r
+ colours.append("COLOUR\t" + row.label + "\t"\r
+ + jalview.util.Format.getHexString(color) + "\n");\r
}\r
\r
}\r
printGroups(groups);\r
}\r
\r
- if(properties!=null)\r
+ if (properties != null)\r
{\r
text.append("\n\nALIGNMENT");\r
Enumeration en = properties.keys();\r
- while(en.hasMoreElements())\r
+ while (en.hasMoreElements())\r
{\r
String key = en.nextElement().toString();\r
- text.append("\t"+key+"="+properties.get(key));\r
+ text.append("\t" + key + "=" + properties.get(key));\r
}\r
\r
}\r
- \r
+\r
return text.toString();\r
}\r
\r
for (int i = 0; i < sequenceGroups.size(); i++)\r
{\r
sg = (SequenceGroup) sequenceGroups.elementAt(i);\r
- text.append("SEQUENCE_GROUP\t"\r
- + sg.getName() + "\t"\r
- + (sg.getStartRes() + 1) + "\t"\r
- + (sg.getEndRes() + 1) + "\t" + "-1\t");\r
+ text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"\r
+ + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1) + "\t"\r
+ + "-1\t");\r
for (int s = 0; s < sg.getSize(); s++)\r
{\r
text.append(sg.getSequenceAt(s).getName() + "\t");\r
}\r
if (sg.cs != null)\r
{\r
- text.append("colour=" + ColourSchemeProperty.getColourName(sg.cs) +\r
- "\t");\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
text.append("consThreshold=" + sg.cs.getConservationInc() + "\t");\r
}\r
}\r
- text.append("outlineColour=" +\r
- jalview.util.Format.getHexString(sg.getOutlineColour()) +\r
- "\t");\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
\r
if (sg.textColour != java.awt.Color.black)\r
{\r
- text.append("textCol1=" +\r
- jalview.util.Format.getHexString(sg.textColour) + "\t");\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
+ text.append("textCol2="\r
+ + jalview.util.Format.getHexString(sg.textColour2) + "\t");\r
}\r
if (sg.thresholdTextColour != 0)\r
{\r
text.append("textColThreshold=" + sg.thresholdTextColour);\r
}\r
- if (sg.idColour!=null)\r
+ if (sg.idColour != null)\r
{\r
- text.append("idColour="+jalview.util.Format.getHexString(sg.idColour)+"\t");\r
+ text.append("idColour="\r
+ + jalview.util.Format.getHexString(sg.idColour) + "\t");\r
}\r
\r
text.append("\n\n");\r
}\r
\r
SequenceI refSeq = null;\r
+\r
String refSeqId = null;\r
- public boolean readAnnotationFile(AlignmentI al,\r
- String file,\r
- String protocol)\r
+\r
+ public boolean readAnnotationFile(AlignmentI al, String file,\r
+ String protocol)\r
{\r
try\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
{\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
+ || line.indexOf("JALVIEW_ANNOTATION") > -1\r
+ || line.length() == 0)\r
{\r
continue;\r
}\r
{\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
+ 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(\r
- "WARNING: SEQUENCE_REF index must be > 0 in AnnotationFile");\r
}\r
}\r
- catch (Exception ex)\r
+ else\r
{\r
- refSeqIndex = 1;\r
- }\r
- } else {\r
refSeq = null;\r
refSeqId = null;\r
}\r
- continue ;\r
+ continue;\r
}\r
\r
else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))\r
continue;\r
}\r
\r
- else if( token.equalsIgnoreCase("BELOW_ALIGNMENT"))\r
+ else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))\r
{\r
setBelowAlignment(al, st);\r
continue;\r
}\r
- else if( token.equalsIgnoreCase("ALIGNMENT"))\r
+ else if (token.equalsIgnoreCase("ALIGNMENT"))\r
{\r
addAlignmentDetails(al, st);\r
continue;\r
graphStyle = AlignmentAnnotation.getGraphValueFromString(token);\r
label = st.nextToken();\r
\r
-\r
index = 0;\r
annotations = new Annotation[alWidth];\r
description = null;\r
float score = Float.NaN;\r
\r
- if(st.hasMoreTokens())\r
+ if (st.hasMoreTokens())\r
{\r
line = st.nextToken();\r
\r
- if (line.indexOf("|") ==-1)\r
+ if (line.indexOf("|") == -1)\r
{\r
description = line;\r
if (st.hasMoreTokens())\r
line = st.nextToken();\r
}\r
\r
- if(st.hasMoreTokens())\r
+ if (st.hasMoreTokens())\r
{\r
- //This must be the score\r
+ // This must be the score\r
score = Float.valueOf(st.nextToken()).floatValue();\r
}\r
\r
st = new StringTokenizer(line, "|", true);\r
\r
-\r
boolean emptyColumn = true;\r
- boolean onlyOneElement = (st.countTokens()==1);\r
+ boolean onlyOneElement = (st.countTokens() == 1);\r
\r
while (st.hasMoreElements() && index < alWidth)\r
{\r
token = st.nextToken().trim();\r
\r
- if(onlyOneElement)\r
+ if (onlyOneElement)\r
{\r
try\r
{\r
score = Float.valueOf(token).floatValue();\r
break;\r
+ } catch (NumberFormatException ex)\r
+ {\r
}\r
- catch(NumberFormatException ex){}\r
}\r
\r
if (token.equals("|"))\r
\r
}\r
\r
- annotation = new AlignmentAnnotation(label,\r
- description,\r
- (index==0) ? null : annotations,\r
- 0,\r
- 0,\r
- graphStyle);\r
+ annotation = new AlignmentAnnotation(label, description,\r
+ (index == 0) ? null : annotations, 0, 0, graphStyle);\r
\r
annotation.score = score;\r
\r
if (refSeq != null)\r
{\r
- annotation.belowAlignment=false;\r
- do {\r
+ annotation.belowAlignment = false;\r
+ do\r
+ {\r
// copy before we do any mapping business.\r
- // TODO: verify that undo/redo with 1:many sequence associated annotations can be undone correctly\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(refSeq, refSeqIndex, false);\r
annotation.adjustForAlignment();\r
refSeq.addAlignmentAnnotation(annotation);\r
al.addAnnotation(annotation);\r
al.setAnnotationIndex(annotation,\r
- al.getAlignmentAnnotation().length - existingAnnotations -\r
- 1);\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 && (refSeq=al.findName(refSeq, refSeqId, true))!=null);\r
- } else {\r
+\r
+ } while (refSeqId != null\r
+ && (refSeq = al.findName(refSeq, refSeqId, true)) != null);\r
+ }\r
+ else\r
+ {\r
al.addAnnotation(annotation);\r
al.setAnnotationIndex(annotation,\r
- al.getAlignmentAnnotation().length - existingAnnotations -\r
- 1);\r
+ al.getAlignmentAnnotation().length - existingAnnotations\r
+ - 1);\r
}\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
float value = 0;\r
boolean parsedValue = false;\r
\r
- //find colour here\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
+ 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
+ colour = ucs.getColourFromString(string.substring(i + 1, j));\r
\r
- string = string.substring(0,i)+string.substring(j+1);\r
+ string = string.substring(0, i) + string.substring(j + 1);\r
}\r
\r
StringTokenizer st = new StringTokenizer(string, ",");\r
value = new Float(token).floatValue();\r
parsedValue = true;\r
continue;\r
+ } catch (NumberFormatException ex)\r
+ {\r
}\r
- catch (NumberFormatException ex)\r
- {}\r
}\r
\r
if (token.equals("H") || token.equals("E"))\r
\r
}\r
\r
- if (displayChar!=null\r
- && displayChar.length() > 1\r
- && desc!=null\r
- && 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 is renderable by any of the applet or application rendering code\r
- * but instead we check for null strings when the display character is rendered. \r
- if (displayChar==null)\r
- {\r
- displayChar="";\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
int graphGroup = -1;\r
String group = st.nextToken();\r
- //First make sure we are not overwriting the graphIndex\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
}\r
}\r
\r
- //Now update groups\r
+ // Now update groups\r
while (st.hasMoreTokens())\r
{\r
group = st.nextToken();\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
-\r
-\r
if (refSeq != null)\r
{\r
sg.setStartRes(refSeq.findIndex(sg.getStartRes() + 1) - 1);\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
+ // 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
sg.cs.setConservationInc(Integer.parseInt(value));\r
Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.getSequences(null),\r
- sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
+ ResidueProperties.propHash, 3, sg.getSequences(null), sg\r
+ .getStartRes(), sg.getEndRes() + 1);\r
\r
c.calculate();\r
c.verdict(false, 25);\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)).findColour('A'));\r
+ sg.setIdColour((def = new UserColourScheme(value))\r
+ .findColour('A'));\r
}\r
sg.recalcConservation();\r
}\r
- if (sg.cs==null)\r
+ if (sg.cs == null)\r
{\r
sg.cs = def;\r
}\r
{\r
String token;\r
AlignmentAnnotation aa;\r
- while(st.hasMoreTokens())\r
+ while (st.hasMoreTokens())\r
{\r
token = st.nextToken();\r
- for(int i=0; i<al.getAlignmentAnnotation().length; i++)\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
+ if (aa.sequenceRef == refSeq && aa.label.equals(token))\r
{\r
aa.belowAlignment = true;\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
+ al.setProperty(key, value);\r
}\r
}\r
\r
/**\r
- * Write annotations as a CSV file of the form 'label, value, value, ...' for each row.\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
+ for (int i = 0; i < annotations.length; i++)\r
{\r
String atos = annotations[i].toString();\r
int p = 0;\r
- do {\r
+ do\r
+ {\r
int cp = atos.indexOf("\n", p);\r
sp.append(annotations[i].label);\r
sp.append(",");\r
- if (cp>p)\r
+ if (cp > p)\r
+ {\r
+ sp.append(atos.substring(p, cp + 1));\r
+ }\r
+ else\r
{\r
- sp.append(atos.substring(p, cp+1));\r
- } else {\r
sp.append(atos.substring(p));\r
sp.append("\n");\r
}\r
- p = cp+1;\r
- } while (p>0);\r
+ p = cp + 1;\r
+ } while (p > 0);\r
}\r
return sp.toString();\r
}\r
git://source.jalview.org / jalview.git / blobdiff