/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 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
- * 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
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview 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 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\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 jalview.schemes.UserColourScheme;\r
-import java.net.URL;\r
\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
\r
public class AnnotationFile\r
{\r
+ public AnnotationFile()\r
+ {\r
+ init();\r
+ }\r
+\r
+ /**\r
+ * character used to write newlines\r
+ */\r
+ protected String newline = System.getProperty("line.separator");\r
+\r
+ /**\r
+ * set new line string and reset the output buffer\r
+ * \r
+ * @param nl\r
+ */\r
+ public void setNewlineString(String nl)\r
+ {\r
+ newline = nl;\r
+ init();\r
+ }\r
+\r
+ public String getNewlineString()\r
+ {\r
+ return newline;\r
+ }\r
+\r
+ StringBuffer text;\r
+\r
+ private void init()\r
+ {\r
+ text = new StringBuffer("JALVIEW_ANNOTATION"+newline + "# Created: "\r
+ + new java.util.Date() + newline + newline);\r
+ refSeq = null;\r
+ refSeqId = null;\r
+ }\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
+ return printAnnotations(annotations, groups, properties, null);\r
+\r
+ }\r
\r
- public String printAnnotations(AlignmentAnnotation [] annotations)\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
- StringBuffer text = new StringBuffer(\r
- "JALVIEW_ANNOTATION\n"\r
- +"# Created: "\r
- +new java.util.Date()+"\n\n");\r
+ public String viewname;\r
\r
- AlignmentAnnotation row;\r
- String comma;\r
- SequenceI seqref = null;\r
+ public HiddenSequences hidseqs;\r
\r
- StringBuffer colours = new StringBuffer();\r
- StringBuffer graphLine = new StringBuffer();\r
+ public ColumnSelection hiddencols;\r
\r
- Hashtable graphGroup = new Hashtable();\r
+ public Vector visibleGroups;\r
\r
- java.awt.Color color;\r
+ public Hashtable hiddenRepSeqs;\r
\r
- for(int i=0; i<annotations.length; i++)\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
+ /**\r
+ * Prepare an annotation file given a set of annotations, groups, alignment\r
+ * properties and views.\r
+ * \r
+ * @param annotations\r
+ * @param groups\r
+ * @param properties\r
+ * @param views\r
+ * @return annotation file\r
+ */\r
+ public String printAnnotations(AlignmentAnnotation[] annotations,\r
+ Vector groups, Hashtable properties, ViewDef[] views)\r
+ {\r
+ // TODO: resolve views issue : annotationFile could contain visible region,\r
+ // or full data + hidden region specifications for a view.\r
+ if (annotations != null)\r
+ {\r
+ boolean oneColour = true;\r
+ AlignmentAnnotation row;\r
+ String comma;\r
+ SequenceI refSeq = null;\r
+ SequenceGroup refGroup = null;\r
+\r
+ StringBuffer colours = new StringBuffer();\r
+ StringBuffer graphLine = new StringBuffer();\r
+ StringBuffer rowprops = new StringBuffer();\r
+ Hashtable graphGroup = new Hashtable();\r
\r
- color = null;\r
+ java.awt.Color color;\r
\r
- if( row.sequenceRef == null)\r
+ for (int i = 0; i < annotations.length; i++)\r
{\r
- if(seqref!=null)\r
- text.append("\nSEQUENCE_REF\tALIGNMENT\n");\r
+ row = annotations[i];\r
\r
- seqref = null;\r
- }\r
+ if (!row.visible && !row.hasScore())\r
+ {\r
+ continue;\r
+ }\r
\r
- else if (seqref == null || seqref != row.sequenceRef)\r
- {\r
- seqref = row.sequenceRef;\r
- text.append("\nSEQUENCE_REF\t" + seqref.getName() + "\n");\r
- }\r
+ color = null;\r
+ oneColour = true;\r
\r
+ if (row.sequenceRef == null)\r
+ {\r
+ if (refSeq != null)\r
+ {\r
+ text.append(newline);\r
+ text.append("SEQUENCE_REF\tALIGNMENT");\r
+ text.append(newline);\r
+ }\r
\r
- if( row.graph == AlignmentAnnotation.NO_GRAPH)\r
- {\r
+ refSeq = null;\r
+ }\r
+\r
+ else\r
+ {\r
+ if (refSeq == null || refSeq != row.sequenceRef)\r
+ {\r
+ refSeq = row.sequenceRef;\r
+ text.append(newline);\r
+ text.append("SEQUENCE_REF\t");\r
+ text.append(refSeq.getName());\r
+ text.append(newline);\r
+ }\r
+ }\r
+ // mark any group references for the row\r
+ if (row.groupRef == null)\r
+ {\r
+\r
+ if (refGroup != null)\r
+ {\r
+ text.append(newline);\r
+ text.append("GROUP_REF\tALIGNMENT");\r
+ text.append(newline);\r
+ }\r
+\r
+ refGroup = null;\r
+ }\r
+ else\r
+ {\r
+ if (refGroup == null || refGroup != row.groupRef)\r
+ {\r
+ refGroup = row.groupRef;\r
+ text.append(newline);\r
+ text.append("GROUP_REF\t");\r
+ text.append(refGroup.getName());\r
+ text.append(newline);\r
+ }\r
+ }\r
+\r
+ boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, hasText = false;\r
+ // lookahead to check what the annotation row object actually contains.\r
+ for (int j = 0; row.annotations != null\r
+ && j < row.annotations.length\r
+ && (!hasGlyphs || !hasLabels || !hasValues); j++)\r
+ {\r
+ if (row.annotations[j] != null)\r
+ {\r
+ hasLabels |= (row.annotations[j].displayCharacter != null\r
+ && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter\r
+ .equals(" "));\r
+ hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');\r
+ hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't\r
+ // be\r
+ // rendered..\r
+ hasText |= (row.annotations[j].description != null && row.annotations[j].description\r
+ .length() > 0);\r
+ }\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
+ hasValues = false; // only secondary structure\r
+ // hasLabels = false; // and annotation description string.\r
+ }\r
+ else\r
+ {\r
+ if (row.graph == AlignmentAnnotation.BAR_GRAPH)\r
+ {\r
+ text.append("BAR_GRAPH\t");\r
+ hasGlyphs = false; // no secondary structure\r
+\r
+ }\r
+ else if (row.graph == AlignmentAnnotation.LINE_GRAPH)\r
+ {\r
+ hasGlyphs = false; // no secondary structure\r
+ text.append("LINE_GRAPH\t");\r
+ }\r
+\r
+ if (row.getThreshold() != null)\r
+ {\r
+ graphLine.append("GRAPHLINE\t");\r
+ graphLine.append(row.label);\r
+ graphLine.append("\t");\r
+ graphLine.append(row.getThreshold().value);\r
+ graphLine.append("\t");\r
+ graphLine.append(row.getThreshold().label);\r
+ graphLine.append("\t");\r
+ graphLine.append(jalview.util.Format.getHexString(row\r
+ .getThreshold().colour));\r
+ graphLine.append(newline);\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
- for(int j=0; j<row.annotations.length; j++)\r
- {\r
- if (seqref != null && jalview.util.Comparison.isGap(seqref.getCharAt(j)))\r
- continue;\r
+ }\r
\r
- if(row.annotations[j]!=null)\r
+ text.append(row.label + "\t");\r
+ if (row.description != null)\r
+ {\r
+ text.append(row.description + "\t");\r
+ }\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 (hasGlyphs) // could be also hasGlyphs || ...\r
+ {\r
+\r
+ text.append(comma);\r
+ if (row.annotations[j].secondaryStructure != ' ')\r
+ {\r
+ // only write out the field if its not whitespace.\r
+ text.append(row.annotations[j].secondaryStructure);\r
+ }\r
+ comma = ",";\r
+ }\r
+ if (hasValues)\r
+ {\r
+ if (row.annotations[j].value != Float.NaN)\r
+ {\r
+ text.append(comma + row.annotations[j].value);\r
+ }\r
+ else\r
+ {\r
+ System.err.println("Skipping NaN - not valid value.");\r
+ text.append(comma + 0f);// row.annotations[j].value);\r
+ }\r
+ comma = ",";\r
+ }\r
+ if (hasLabels)\r
+ {\r
+ // TODO: labels are emitted after values for bar graphs.\r
+ if // empty labels are allowed, so\r
+ (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 (hasText)\r
+ {\r
+ if (row.annotations[j].description != null\r
+ && row.annotations[j].description.length() > 0\r
+ && !row.annotations[j].description\r
+ .equals(row.annotations[j].displayCharacter))\r
+ {\r
+ text.append(comma + row.annotations[j].description);\r
+ comma = ",";\r
+ }\r
+ }\r
+ if (color != null && !color.equals(row.annotations[j].colour))\r
+ {\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
+\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
+ comma = ",";\r
+ }\r
}\r
+ text.append("|");\r
+ }\r
+\r
+ if (row.hasScore())\r
+ text.append("\t" + row.score);\r
+\r
+ text.append(newline);\r
+\r
+ if (color != null && color != java.awt.Color.black && oneColour)\r
+ {\r
+ colours.append("COLOUR\t");\r
+ colours.append(row.label);\r
+ colours.append("\t");\r
+ colours.append(jalview.util.Format.getHexString(color));\r
+ colours.append(newline);\r
+ }\r
+ if (row.scaleColLabel || row.showAllColLabels\r
+ || row.centreColLabels)\r
+ {\r
+ rowprops.append("ROWPROPERTIES\t");\r
+ rowprops.append(row.label);\r
+ rowprops.append("\tscaletofit=");\r
+ rowprops.append(row.scaleColLabel);\r
+ rowprops.append("\tshowalllabs=");\r
+ rowprops.append(row.showAllColLabels);\r
+ rowprops.append("\tcentrelabs=");\r
+ rowprops.append(row.centreColLabels);\r
+ rowprops.append(newline);\r
}\r
- text.append("|");\r
}\r
\r
- text.append("\n");\r
+ text.append(newline);\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());\r
+ text.append(newline);\r
+ }\r
}\r
-\r
+ text.append(rowprops.toString());\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(newline);\r
+ text.append(newline);\r
+ text.append("ALIGNMENT");\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");\r
+ text.append(key);\r
+ text.append("=");\r
+ text.append(properties.get(key));\r
}\r
+ // TODO: output alignment visualization settings here if required\r
+\r
}\r
\r
return text.toString();\r
}\r
\r
- public boolean readAnnotationFile(AlignmentI al, String file)\r
+ public void printGroups(Vector sequenceGroups)\r
{\r
- try\r
+ SequenceGroup sg;\r
+ SequenceI seqrep = null;\r
+ for (int i = 0; i < sequenceGroups.size(); i++)\r
{\r
- BufferedReader in = null;\r
- java.io.InputStream is = getClass().getResourceAsStream("/" + file);\r
- if (is != null)\r
+ sg = (SequenceGroup) sequenceGroups.elementAt(i);\r
+ if (!sg.hasSeqrep())\r
{\r
- in = new BufferedReader(new java.io.InputStreamReader(is));\r
+ text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"\r
+ + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1)\r
+ + "\t" + "-1\t");\r
+ seqrep = null;\r
}\r
else\r
{\r
- try\r
+ seqrep = sg.getSeqrep();\r
+ text.append("SEQUENCE_REF\t");\r
+ text.append(seqrep.getName());\r
+ text.append(newline);\r
+ text.append("SEQUENCE_GROUP\t");\r
+ text.append(sg.getName());\r
+ text.append("\t");\r
+ text.append((seqrep.findPosition(sg.getStartRes())));\r
+ text.append("\t");\r
+ text.append((seqrep.findPosition(sg.getEndRes())));\r
+ text.append("\t");\r
+ text.append("-1\t");\r
+ }\r
+ for (int s = 0; s < sg.getSize(); s++)\r
+ {\r
+ text.append(sg.getSequenceAt(s).getName());\r
+ text.append("\t");\r
+ }\r
+ text.append(newline);\r
+ text.append("PROPERTIES\t");\r
+ text.append(sg.getName());\r
+ text.append("\t");\r
+\r
+ if (sg.getDescription() != null)\r
+ {\r
+ text.append("description=");\r
+ text.append(sg.getDescription());\r
+ text.append("\t");\r
+ }\r
+ if (sg.cs != null)\r
+ {\r
+ text.append("colour=");\r
+ text.append(ColourSchemeProperty.getColourName(sg.cs));\r
+ text.append("\t");\r
+ if (sg.cs.getThreshold() != 0)\r
{\r
- URL url = new URL(file);\r
- in = new BufferedReader(new InputStreamReader(url.openStream()));\r
+ text.append("pidThreshold=");\r
+ text.append(sg.cs.getThreshold());\r
}\r
- catch (java.net.MalformedURLException ex)\r
+ if (sg.cs.conservationApplied())\r
+ {\r
+ text.append("consThreshold=");\r
+ text.append(sg.cs.getConservationInc());\r
+ text.append("\t");\r
+ }\r
+ }\r
+ text.append("outlineColour=");\r
+ text.append(jalview.util.Format.getHexString(sg.getOutlineColour()));\r
+ text.append("\t");\r
+\r
+ text.append("displayBoxes=");\r
+ text.append(sg.getDisplayBoxes());\r
+ text.append("\t");\r
+ text.append("displayText=");\r
+ text.append(sg.getDisplayText());\r
+ text.append("\t");\r
+ text.append("colourText=");\r
+ text.append(sg.getColourText());\r
+ text.append("\t");\r
+ text.append("showUnconserved=");\r
+ text.append(sg.getShowNonconserved());\r
+ text.append("\t");\r
+ if (sg.textColour != java.awt.Color.black)\r
+ {\r
+ text.append("textCol1=");\r
+ text.append(jalview.util.Format.getHexString(sg.textColour));\r
+ text.append("\t");\r
+ }\r
+ if (sg.textColour2 != java.awt.Color.white)\r
+ {\r
+ text.append("textCol2=");\r
+ text.append(jalview.util.Format.getHexString(sg.textColour2));\r
+ text.append("\t");\r
+ }\r
+ if (sg.thresholdTextColour != 0)\r
+ {\r
+ text.append("textColThreshold=");\r
+ text.append(sg.thresholdTextColour);\r
+ text.append("\t");\r
+ }\r
+ if (sg.idColour != null)\r
+ {\r
+ text.append("idColour=");\r
+ text.append(jalview.util.Format.getHexString(sg.idColour));\r
+ text.append("\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(newline);\r
+ text.append("SEQUENCE_REF");\r
+ }\r
+ text.append(newline);\r
+ text.append(newline);\r
+\r
+ }\r
+ }\r
+\r
+ SequenceI refSeq = null;\r
+\r
+ String refSeqId = null;\r
+\r
+ public boolean readAnnotationFile(AlignmentI al, String file,\r
+ String protocol)\r
+ {\r
+ BufferedReader in = null;\r
+ try\r
+ {\r
+ if (protocol.equals(AppletFormatAdapter.FILE))\r
+ {\r
+ in = new BufferedReader(new FileReader(file));\r
+ }\r
+ else if (protocol.equals(AppletFormatAdapter.URL))\r
+ {\r
+ URL url = new URL(file);\r
+ in = new BufferedReader(new InputStreamReader(url.openStream()));\r
+ }\r
+ else if (protocol.equals(AppletFormatAdapter.PASTE))\r
+ {\r
+ in = new BufferedReader(new StringReader(file));\r
+ }\r
+ else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))\r
+ {\r
+ java.io.InputStream is = getClass().getResourceAsStream("/" + file);\r
+ if (is != null)\r
{\r
- in = new BufferedReader(new FileReader(file));\r
+ in = new BufferedReader(new java.io.InputStreamReader(is));\r
}\r
}\r
+ if (in != null)\r
+ {\r
+ return parseAnnotationFrom(al, in);\r
+ }\r
+\r
+ } catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ System.out.println("Problem reading annotation file: " + ex);\r
+ return false;\r
+ }\r
+ return false;\r
+ }\r
+\r
+ public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in)\r
+ throws Exception\r
+ {\r
+ boolean modified = false;\r
+ String groupRef = null;\r
+ Hashtable groupRefRows = new Hashtable();\r
\r
+ Hashtable autoAnnots = new Hashtable();\r
+ {\r
String line, label, description, token;\r
int graphStyle, index;\r
- SequenceI refSeq = null;\r
int refSeqIndex = 1;\r
int existingAnnotations = 0;\r
- if(al.getAlignmentAnnotation()!=null)\r
- existingAnnotations = al.getAlignmentAnnotation().length;\r
+ // when true - will add new rows regardless of whether they are duplicate\r
+ // auto-annotation like consensus or conservation graphs\r
+ boolean overrideAutoAnnot = false;\r
+ if (al.getAlignmentAnnotation() != null)\r
+ {\r
+ existingAnnotations = al.getAlignmentAnnotation().length;\r
+ if (existingAnnotations > 0)\r
+ {\r
+ AlignmentAnnotation[] aa = al.getAlignmentAnnotation();\r
+ for (int aai = 0; aai < aa.length; aai++)\r
+ {\r
+ if (aa[aai].autoCalculated)\r
+ {\r
+ // make a note of the name and description\r
+ autoAnnots.put(\r
+ autoAnnotsKey(aa[aai], aa[aai].sequenceRef,\r
+ (aa[aai].groupRef == null ? null\r
+ : aa[aai].groupRef.getName())),\r
+ new Integer(1));\r
+ }\r
+ }\r
+ }\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
+ modified = true;\r
continue;\r
}\r
\r
- if(token.equalsIgnoreCase("COMBINE") )\r
+ else if (token.equalsIgnoreCase("COMBINE"))\r
{\r
combineAnnotations(al, st);\r
+ modified = true;\r
continue;\r
}\r
-\r
- if (token.equalsIgnoreCase("GRAPHLINE"))\r
+ else if (token.equalsIgnoreCase("ROWPROPERTIES"))\r
+ {\r
+ addRowProperties(al, st);\r
+ modified = true;\r
+ continue;\r
+ }\r
+ else if (token.equalsIgnoreCase("GRAPHLINE"))\r
{\r
addLine(al, st);\r
+ modified = true;\r
continue;\r
}\r
\r
-\r
- 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
+ refSeq = null;\r
+ refSeqId = null;\r
+ }\r
+ continue;\r
+ }\r
+ else if (token.equalsIgnoreCase("GROUP_REF"))\r
+ {\r
+ // Group references could be forward or backwards, so they are\r
+ // resolved after the whole file is read in\r
+ groupRef = null;\r
+ if (st.hasMoreTokens())\r
{\r
- refSeqIndex = 1;\r
+ groupRef = st.nextToken();\r
+ if (groupRef.length() < 1)\r
+ {\r
+ groupRef = null; // empty string\r
+ }\r
+ else\r
+ {\r
+ if (groupRefRows.get(groupRef) == null)\r
+ {\r
+ groupRefRows.put(groupRef, new Vector());\r
+ }\r
+ }\r
}\r
+ continue;\r
+ }\r
+ else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))\r
+ {\r
+ addGroup(al, st);\r
+ continue;\r
+ }\r
\r
+ else if (token.equalsIgnoreCase("PROPERTIES"))\r
+ {\r
+ addProperties(al, st);\r
+ modified = true;\r
continue;\r
}\r
\r
+ else if (token.equalsIgnoreCase("BELOW_ALIGNMENT"))\r
+ {\r
+ setBelowAlignment(al, st);\r
+ modified = true;\r
+ continue;\r
+ }\r
+ else if (token.equalsIgnoreCase("ALIGNMENT"))\r
+ {\r
+ addAlignmentDetails(al, st);\r
+ modified = true;\r
+ continue;\r
+ }\r
\r
+ // Parse out the annotation row\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
- {\r
- if(emptyColumn)\r
- index++;\r
+ line = st.nextToken();\r
\r
- emptyColumn = true;\r
+ if (line.indexOf("|") == -1)\r
+ {\r
+ description = line;\r
+ if (st.hasMoreTokens())\r
+ line = st.nextToken();\r
}\r
- else\r
+\r
+ if (st.hasMoreTokens())\r
{\r
- annotations[index++] = parseAnnotation(token);\r
- emptyColumn = false;\r
+ // This must be the score\r
+ score = Float.valueOf(st.nextToken()).floatValue();\r
}\r
- }\r
\r
- annotation = new AlignmentAnnotation(label,\r
- description,\r
- annotations,\r
- 0,\r
- 0,\r
- graphStyle);\r
+ st = new StringTokenizer(line, "|", true);\r
\r
- if(refSeq!=null)\r
- {\r
- annotation.createSequenceMapping(refSeq, refSeqIndex, false);\r
- refSeq.addAlignmentAnnotation(annotation);\r
- }\r
+ boolean emptyColumn = true;\r
+ boolean onlyOneElement = (st.countTokens() == 1);\r
\r
- al.addAnnotation(annotation);\r
+ while (st.hasMoreElements() && index < alWidth)\r
+ {\r
+ token = st.nextToken().trim();\r
\r
- al.setAnnotationIndex(annotation, al.getAlignmentAnnotation().length - existingAnnotations-1);\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
- }catch(Exception ex)\r
- {\r
- ex.printStackTrace();\r
- System.out.println("Problem reading annotation file: "+ex);\r
- return false;\r
- }\r
- return true;\r
- }\r
+ if (token.equals("|"))\r
+ {\r
+ if (emptyColumn)\r
+ {\r
+ index++;\r
+ }\r
\r
- Annotation parseAnnotation(String string)\r
+ emptyColumn = true;\r
+ }\r
+ else\r
+ {\r
+ annotations[index++] = parseAnnotation(token, graphStyle);\r
+ emptyColumn = false;\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ annotation = new AlignmentAnnotation(label, description,\r
+ (index == 0) ? null : annotations, 0, 0, graphStyle);\r
+\r
+ annotation.score = score;\r
+ if (!overrideAutoAnnot\r
+ && autoAnnots.containsKey(autoAnnotsKey(annotation, refSeq,\r
+ groupRef)))\r
+ {\r
+ // skip - we've already got an automatic annotation of this type.\r
+ continue;\r
+ }\r
+ // otherwise add it!\r
+ if (refSeq != null)\r
+ {\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\r
+ .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
+ if (groupRef != null)\r
+ {\r
+ ((Vector) groupRefRows.get(groupRef)).addElement(annotation);\r
+ }\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
+ if (groupRef != null)\r
+ {\r
+ ((Vector) groupRefRows.get(groupRef)).addElement(annotation);\r
+ }\r
+ }\r
+ // and set modification flag\r
+ modified = true;\r
+ }\r
+ // Finally, resolve the groupRefs\r
+ Enumeration en = groupRefRows.keys();\r
+ SequenceGroup theGroup = null;\r
+\r
+ while (en.hasMoreElements())\r
+ {\r
+ groupRef = (String) en.nextElement();\r
+ boolean matched = false;\r
+ // Resolve group: TODO: add a getGroupByName method to alignments\r
+ Vector grps = al.getGroups();\r
+ for (int g = 0, gSize = grps.size(); g < gSize; g++)\r
+ {\r
+ theGroup = (SequenceGroup) grps.elementAt(g);\r
+ if (theGroup.getName().equals(groupRef))\r
+ {\r
+ if (matched)\r
+ {\r
+ // TODO: specify and implement duplication of alignment annotation\r
+ // for multiple group references.\r
+ System.err\r
+ .println("Ignoring 1:many group reference mappings for group name '"\r
+ + groupRef + "'");\r
+ }\r
+ else\r
+ {\r
+ matched = true;\r
+ Vector rowset = (Vector) groupRefRows.get(groupRef);\r
+ if (rowset != null && rowset.size() > 0)\r
+ {\r
+ AlignmentAnnotation alan = null;\r
+ for (int elm = 0, elmSize = rowset.size(); elm < elmSize; elm++)\r
+ {\r
+ alan = (AlignmentAnnotation) rowset.elementAt(elm);\r
+ alan.groupRef = theGroup;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ ((Vector) groupRefRows.get(groupRef)).removeAllElements();\r
+ }\r
+ }\r
+ return modified;\r
+ }\r
+\r
+ private Object autoAnnotsKey(AlignmentAnnotation annotation,\r
+ SequenceI refSeq, String groupRef)\r
{\r
- String desc = null, displayChar="";\r
+ return annotation.graph + "\t" + annotation.label + "\t"\r
+ + annotation.description + "\t"\r
+ + (refSeq != null ? refSeq.getDisplayId(true) : "");\r
+ }\r
+\r
+ Annotation parseAnnotation(String string, int graphStyle)\r
+ {\r
+ boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't\r
+ // do the\r
+ // glyph\r
+ // test\r
+ // if we\r
+ // don't\r
+ // want\r
+ // secondary\r
+ // structure\r
+ String desc = null, displayChar = null;\r
char ss = ' '; // secondaryStructure\r
float value = 0;\r
- boolean parsedValue = false;\r
- StringTokenizer st = new StringTokenizer(string, ",");\r
+ boolean parsedValue = false, dcset = 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
+ if (i > 0 && string.charAt(i - 1) == ',')\r
+ {\r
+ // clip the preceding comma as well\r
+ i--;\r
+ }\r
+ string = string.substring(0, i) + string.substring(j + 1);\r
+ }\r
+\r
+ StringTokenizer st = new StringTokenizer(string, ",", true);\r
String token;\r
- while(st.hasMoreTokens())\r
+ boolean seenContent = false;\r
+ int pass = 0;\r
+ while (st.hasMoreTokens())\r
{\r
+ pass++;\r
token = st.nextToken().trim();\r
- if(token.length()==0)\r
+ if (token.equals(","))\r
+ {\r
+ if (!seenContent && parsedValue && !dcset)\r
+ {\r
+ // allow the value below the bar/line to be empty\r
+ dcset = true;\r
+ displayChar = " ";\r
+ }\r
+ seenContent = false;\r
continue;\r
+ }\r
+ else\r
+ {\r
+ seenContent = true;\r
+ }\r
\r
- if(!parsedValue)\r
+ if (!parsedValue)\r
{\r
- try{\r
+ try\r
+ {\r
displayChar = token;\r
+ // foo\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
+ else\r
+ {\r
+ if (token.length() == 1)\r
+ {\r
+ displayChar = token;\r
+ }\r
+ }\r
+ if (hasSymbols\r
+ && (token.equals("H") || token.equals("E") || token.equals("S") || token\r
+ .equals(" ")))\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 || (parsedValue && pass > 2))\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 (!dcset && string.charAt(string.length() - 1) == ',')\r
+ // {\r
+ // displayChar = " "; // empty display char symbol.\r
+ // }\r
+ if (displayChar != null && desc != null && desc.length() == 1)\r
{\r
- String tmp = displayChar;\r
- displayChar = desc;\r
- desc = tmp;\r
+ if (displayChar.length() > 1)\r
+ {\r
+ // switch desc and displayChar - legacy support\r
+ String tmp = displayChar;\r
+ displayChar = desc;\r
+ desc = tmp;\r
+ }\r
+ else\r
+ {\r
+ if (displayChar.equals(desc))\r
+ {\r
+ // duplicate label - hangover from the 'robust parser' above\r
+ desc = null;\r
+ }\r
+ }\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
- {\r
- if(al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
- {\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
+ // First make sure we are not overwriting the graphIndex\r
+ if (al.getAlignmentAnnotation() != null)\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
+ 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
+ {\r
+ group = st.nextToken();\r
+ for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
+ {\r
+ if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
+ {\r
+ al.getAlignmentAnnotation()[i].graphGroup = graphGroup;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ System.err\r
+ .println("Couldn't combine annotations. None are added to alignment yet!");\r
}\r
}\r
\r
void addLine(AlignmentI al, StringTokenizer st)\r
{\r
String group = st.nextToken();\r
- AlignmentAnnotation annotation = null;\r
-\r
- for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
+ AlignmentAnnotation annotation = null, alannot[] = al\r
+ .getAlignmentAnnotation();\r
+ if (alannot != null)\r
{\r
- if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
+ for (int i = 0; i < alannot.length; i++)\r
{\r
- annotation = al.getAlignmentAnnotation()[i];\r
- break;\r
+ if (alannot[i].label.equalsIgnoreCase(group))\r
+ {\r
+ annotation = alannot[i];\r
+ break;\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
\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
+ String rng = "";\r
+ try\r
+ {\r
+ rng = st.nextToken();\r
+ if (rng.length() > 0 && !rng.startsWith("*"))\r
+ {\r
+ sg.setStartRes(Integer.parseInt(rng) - 1);\r
+ }\r
+ else\r
+ {\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
+ }\r
+ else\r
+ {\r
+ sg.setEndRes(al.getWidth() - 1);\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"\r
+ + 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
+ {\r
+ while (st.hasMoreElements())\r
+ {\r
+ sg.addSequence(al.findName(st.nextToken()), false);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ StringTokenizer st2 = new StringTokenizer(index, ",");\r
\r
+ while (st2.hasMoreTokens())\r
+ {\r
+ String tmp = st2.nextToken();\r
+ if (tmp.equals("*"))\r
+ {\r
+ for (int i = 0; i < al.getHeight(); i++)\r
+ {\r
+ sg.addSequence(al.getSequenceAt(i), false);\r
+ }\r
+ }\r
+ else if (tmp.indexOf("-") >= 0)\r
+ {\r
+ StringTokenizer st3 = new StringTokenizer(tmp, "-");\r
+\r
+ int start = (Integer.parseInt(st3.nextToken()));\r
+ int end = (Integer.parseInt(st3.nextToken()));\r
+\r
+ if (end > start)\r
+ {\r
+ for (int i = start; i <= end; i++)\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
+ }\r
+ }\r
+ }\r
+\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.setSeqrep(refSeq);\r
+ }\r
+\r
+ if (sg.getSize() > 0)\r
+ {\r
+ al.addGroup(sg);\r
+ }\r
+ }\r
+\r
+ void addRowProperties(AlignmentI al, StringTokenizer st)\r
+ {\r
+ String label = st.nextToken(), keyValue, key, value;\r
+ boolean scaletofit = false, centerlab = false, showalllabs = false;\r
+ while (st.hasMoreTokens())\r
+ {\r
+ keyValue = st.nextToken();\r
+ key = keyValue.substring(0, keyValue.indexOf("="));\r
+ value = keyValue.substring(keyValue.indexOf("=") + 1);\r
+ if (key.equalsIgnoreCase("scaletofit"))\r
+ {\r
+ scaletofit = Boolean.valueOf(value).booleanValue();\r
+ }\r
+ if (key.equalsIgnoreCase("showalllabs"))\r
+ {\r
+ showalllabs = Boolean.valueOf(value).booleanValue();\r
+ }\r
+ if (key.equalsIgnoreCase("centrelabs"))\r
+ {\r
+ centerlab = Boolean.valueOf(value).booleanValue();\r
+ }\r
+ AlignmentAnnotation[] alr = al.getAlignmentAnnotation();\r
+ if (alr != null)\r
+ {\r
+ for (int i = 0; i < alr.length; i++)\r
+ {\r
+ if (alr[i].label.equalsIgnoreCase(label))\r
+ {\r
+ alr[i].centreColLabels = centerlab;\r
+ alr[i].scaleColLabel = scaletofit;\r
+ alr[i].showAllColLabels = showalllabs;\r
+ }\r
+ }\r
+ }\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
+ 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
+ {\r
+ String keyValue, key, value;\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
+\r
+ if (key.equalsIgnoreCase("description"))\r
+ {\r
+ sg.setDescription(value);\r
+ }\r
+ else if (key.equalsIgnoreCase("colour"))\r
+ {\r
+ sg.cs = ColourSchemeProperty.getColour(al, value);\r
+ }\r
+ else if (key.equalsIgnoreCase("pidThreshold"))\r
+ {\r
+ sg.cs.setThreshold(Integer.parseInt(value), true);\r
+\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),\r
+ sg.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
+ {\r
+ sg.setDisplayBoxes(Boolean.valueOf(value).booleanValue());\r
+ }\r
+ else if (key.equalsIgnoreCase("showUnconserved"))\r
+ {\r
+ sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());\r
+ }\r
+ else if (key.equalsIgnoreCase("displayText"))\r
+ {\r
+ sg.setDisplayText(Boolean.valueOf(value).booleanValue());\r
+ }\r
+ else if (key.equalsIgnoreCase("colourText"))\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
+ else if (key.equalsIgnoreCase("textCol2"))\r
+ {\r
+ sg.textColour2 = new UserColourScheme(value).findColour('A');\r
+ }\r
+ else if (key.equalsIgnoreCase("textColThreshold"))\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, ala[] = al.getAlignmentAnnotation();\r
+ if (ala == null)\r
+ {\r
+ System.err\r
+ .print("Warning - no annotation to set below for sequence associated annotation:");\r
+ }\r
+ while (st.hasMoreTokens())\r
+ {\r
+ token = st.nextToken();\r
+ if (ala == null)\r
+ {\r
+ System.err.print(" " + token);\r
+ }\r
+ else\r
+ {\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
+ if (ala == null)\r
+ {\r
+ System.err.print("\n");\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(newline);\r
+ }\r
+ p = cp + 1;\r
+ } while (p > 0);\r
+ }\r
+ return sp.toString();\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff