/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.GraphLine;
import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.UserColourScheme;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.ColorUtils;
+import java.awt.Color;
import java.io.BufferedReader;
+import java.io.File;
import java.io.FileReader;
import java.io.InputStreamReader;
import java.io.StringReader;
&& row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter
.equals(" "));
hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');
- hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't
+ hasValues |= (!Float.isNaN(row.annotations[j].value)); // NaNs can't
// be
// rendered..
hasText |= (row.annotations[j].description != null && row.annotations[j].description
}
else
{
- graphGroup_refs.put(key, new Object[]
- { refSeq, refGroup });
+ graphGroup_refs.put(key, new Object[] { refSeq, refGroup });
graphGroup.put(key, row.label);
}
}
}
if (hasValues)
{
- if (row.annotations[j].value != Float.NaN)
+ if (!Float.isNaN(row.annotations[j].value))
{
text.append(comma + row.annotations[j].value);
}
else
{
- System.err.println("Skipping NaN - not valid value.");
+ // System.err.println("Skipping NaN - not valid value.");
text.append(comma + 0f);// row.annotations[j].value);
}
comma = ",";
text.append(properties.get(key));
}
// TODO: output alignment visualization settings here if required
- // iterate through one or more views, defining, marking columns and rows as visible/hidden, and emmitting view properties.
- // View specific annotation is
+ // iterate through one or more views, defining, marking columns and rows
+ // as visible/hidden, and emmitting view properties.
+ // View specific annotation is
}
return text.toString();
if (sg.cs != null)
{
text.append("colour=");
- text.append(ColourSchemeProperty.getColourName(sg.cs));
+ text.append(sg.cs.toString());
text.append("\t");
if (sg.cs.getThreshold() != 0)
{
String refSeqId = null;
public boolean annotateAlignmentView(AlignViewportI viewport,
- String file, String protocol)
+ String file, DataSourceType protocol)
{
ColumnSelection colSel = viewport.getColumnSelection();
if (colSel == null)
}
boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel,
file, protocol);
- if (rslt
- && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
+ if (rslt && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
{
viewport.setColumnSelection(colSel);
}
return rslt;
}
+
public boolean readAnnotationFile(AlignmentI al, String file,
- String protocol)
+ DataSourceType sourceType)
{
- return readAnnotationFile(al, null, file, protocol);
+ return readAnnotationFile(al, null, file, sourceType);
}
public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
- String file, String protocol)
+ String file, DataSourceType sourceType)
{
+ baseUri = "";
BufferedReader in = null;
try
{
- if (protocol.equals(AppletFormatAdapter.FILE))
+ if (sourceType == DataSourceType.FILE)
{
in = new BufferedReader(new FileReader(file));
+ baseUri = new File(file).getParent();
+ if (baseUri == null)
+ {
+ baseUri = "";
+ }
+ else
+ {
+ baseUri += "/";
+ }
}
- else if (protocol.equals(AppletFormatAdapter.URL))
+ else if (sourceType == DataSourceType.URL)
{
URL url = new URL(file);
in = new BufferedReader(new InputStreamReader(url.openStream()));
+ String bs = url.toExternalForm();
+ baseUri = bs.substring(0, bs.indexOf(url.getHost())
+ + url.getHost().length());
+ baseUri += url.toURI().getPath();
+ if (baseUri.lastIndexOf("/") > -1)
+ {
+ baseUri = baseUri.substring(0, baseUri.lastIndexOf("/")) + "/";
+ }
}
- else if (protocol.equals(AppletFormatAdapter.PASTE))
+ else if (sourceType == DataSourceType.PASTE)
{
in = new BufferedReader(new StringReader(file));
+ // TODO - support mimencoded PDBs for a paste.. ?
+ baseUri = "";
}
- else if (protocol.equals(AppletFormatAdapter.CLASSLOADER))
+ else if (sourceType == DataSourceType.CLASSLOADER)
{
java.io.InputStream is = getClass().getResourceAsStream("/" + file);
if (is != null)
{
in = new BufferedReader(new java.io.InputStreamReader(is));
+ // TODO: this probably doesn't work for classloader - needs a test
+ baseUri = new File("/" + file).getParent() + "/";
}
}
if (in != null)
String lastread = "";
- private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
+ /**
+ * used for resolving absolute references to resources relative to
+ * annotationFile location
+ */
+ String baseUri = "";
+
+ private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE",
+ STRUCTMODEL = "STRUCTMODEL";
public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
- BufferedReader in)
- throws Exception
+ BufferedReader in) throws Exception
{
nlinesread = 0;
ArrayList<Object[]> combineAnnotation_calls = new ArrayList<Object[]>();
else if (token.equalsIgnoreCase(COMBINE))
{
// keep a record of current state and resolve groupRef at end
- combineAnnotation_calls.add(new Object[]
- { st, refSeq, groupRef });
+ combineAnnotation_calls
+ .add(new Object[] { st, refSeq, groupRef });
modified = true;
continue;
}
else if (token.equalsIgnoreCase(GRAPHLINE))
{
// resolve at end
- deferredAnnotation_calls.add(new Object[]
- { GRAPHLINE, st, refSeq, groupRef });
+ deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st,
+ refSeq, groupRef });
modified = true;
continue;
}
modified = true;
continue;
}
-
+ else if (token.equalsIgnoreCase(STRUCTMODEL))
+ {
+ boolean failedtoadd = true;
+ // expect
+ // STRUCTMODEL <Query> <TemplateSeqId> <ModelFile> <FastaMappingFile>
+ // <Confidence> <%.I.D>
+ // <MatchStart> <MatchEnd> <Coverage> [<Other Information>]
+ String querySeqId = !st.hasMoreTokens() ? "" : st.nextToken();
+ SequenceI querySeq = al.findName(querySeqId);
+ if (st.hasMoreTokens()) {
+ refSeq = al.findName(refSeqId = st.nextToken());
+ if (refSeq == null)
+ {
+ System.err.println("Couldn't locate " + refSeqId
+ + " in the alignment for STRUCTMODEL");
+ refSeqId = null;
+ }
+ else
+ {
+ String tempId = st.nextToken();
+ String fastaMapping = st.nextToken();
+ String confidence = !st.hasMoreTokens() ? "" : 100
+ * Double.valueOf(st.nextToken()) + "";
+ String pid = !st.hasMoreTokens() ? "" : st.nextToken();
+ String alignRange = !st.hasMoreTokens() ? "" : st.nextToken()
+ + "-" + st.nextToken();
+ String otherInfo = !st.hasMoreTokens() ? "" : st.nextToken();
+ String coverage = "";
+ if (add_structmodel(al, querySeq, refSeq, tempId,
+ fastaMapping,
+ alignRange, coverage,
+ confidence, pid, otherInfo))
+ {
+ failedtoadd = false;
+ }
+ }
+ }
+ if (failedtoadd)
+ {
+ System.err
+ .println("Need <Query> <TemplateSeqId> <ModelFile> <FastaMappingFile> <Confidence> <%.I.D> <MatchStart> <MatchEnd> <Coverage> [<Other Information>] as tab separated fields after"
+ + STRUCTMODEL
+ + ".\nNote: other information could be provided in html format ");
+ } else {
+ modified = true;
+ }
+ continue;
+ }
// Parse out the annotation row
graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
label = st.nextToken();
(SequenceI) _deferred_args[2], // refSeq
(_deferred_args[3] == null) ? null : groupRefLookup
.get(_deferred_args[3]) // the reference
- // group, or null
+ // group, or null
);
}
}
(SequenceI) _combine_args[1], // refSeq
(_combine_args[2] == null) ? null : groupRefLookup
.get(_combine_args[2]) // the reference group,
- // or null
+ // or null
);
}
}
return modified;
}
+ /**
+ * resolve a structural model and generate and add an alignment sequence for
+ * it
+ *
+ * @param refSeq2
+ * @param tempId
+ * @param urlToModel
+ * @param urlToPairwise
+ * @return true if model and sequence was added
+ */
+ private boolean add_structmodel(AlignmentI al, SequenceI querySequence,
+ SequenceI templateSeq,
+ String modelFile, String fastaFile, String aRange,
+ String coverage, String confidence,
+ String pid, String otherInfo)
+ {
+ String warningMessage = null;
+ boolean added = false;
+ try {
+ String structureModelFile = resolveAbsolute(modelFile);
+ String fastaMappingFile = resolveAbsolute(fastaFile.replaceAll(
+ ".fasta.jal", ".fasta"));
+ // System.out.println("Model File >> " + structureModelFile);
+ // System.out.println("Fasta File >> " + fastaMappingFile);
+ PDBEntry phyre2PDBEntry = new PDBEntry(modelFile, null, Type.FILE,
+ structureModelFile);
+ String phyre2ModelDesc = generatePhyre2InfoHTMLTable(aRange,
+ coverage, confidence, pid, otherInfo);
+ phyre2PDBEntry.setProperty("PHYRE2_MODEL_INFO", phyre2ModelDesc);
+ templateSeq.getDatasetSequence().addPDBId(phyre2PDBEntry);
+ if (querySequence != null)
+ {
+ querySequence.getDatasetSequence().addPDBId(phyre2PDBEntry);
+ }
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.registerPhyre2Template(structureModelFile, fastaMappingFile);
+ added = true;
+
+ } catch (Exception x)
+ {
+ warningMessage = x.toString();
+ } finally {
+ if (warningMessage !=null)
+ {
+ System.err.println("Warnings whilst processing STRUCTMODEL: "+warningMessage);
+ }
+ }
+ return added;
+ }
+
+ private String generatePhyre2InfoHTMLTable(String aRange,
+ String coverage, String confidence, String pid, String otherInfo)
+ {
+ StringBuilder phyre2InfoBuilder = new StringBuilder();
+ phyre2InfoBuilder.append("<html><table border=\"1\" width=100%>");
+ phyre2InfoBuilder
+ .append("<tr><td colspan=\"2\"><strong>Phyre2 Template Info</strong></td></tr>");
+ if (aRange != null && !aRange.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("Aligned range")
+ .append("</td><td>").append(aRange).append("</td></tr>");
+ }
+ if (coverage != null && !coverage.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("Coverage")
+ .append("</td><td>").append(coverage).append("</td></tr>");
+ }
+ if (confidence != null && !confidence.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("Confidence")
+ .append("</td><td>").append(confidence).append("</td></tr>");
+ }
+ if (pid != null && !pid.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("%.i.d")
+ .append("</td><td>").append(pid).append("</td></tr>");
+ }
+ if (otherInfo != null && !otherInfo.isEmpty())
+ {
+ phyre2InfoBuilder.append("<tr><td>").append("Other information")
+ .append("</td><td>").append(otherInfo).append("</td></tr>");
+ }
+ phyre2InfoBuilder.append("</table></html>");
+ return phyre2InfoBuilder.toString();
+ }
+
+ private String resolveAbsolute(String relURI)
+ {
+ if (relURI.indexOf(":/") > -1 || relURI.startsWith("/")
+ || "".equals(baseUri) || relURI.startsWith(baseUri))
+ {
+ return relURI;
+ }
+ return baseUri + relURI;
+ }
+
private void parseHideCols(ColumnSelection colSel, String nextToken)
{
- StringTokenizer inval = new StringTokenizer(nextToken,",");
+ StringTokenizer inval = new StringTokenizer(nextToken, ",");
while (inval.hasMoreTokens())
{
String range = inval.nextToken().trim();
Annotation parseAnnotation(String string, int graphStyle)
{
- boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't
- // do the
- // glyph
- // test
- // if we
- // don't
- // want
- // secondary
- // structure
+ // don't do the glyph test if we don't want secondary structure
+ boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH);
String desc = null, displayChar = null;
char ss = ' '; // secondaryStructure
float value = 0;
boolean parsedValue = false, dcset = false;
// find colour here
- java.awt.Color colour = null;
+ Color colour = null;
int i = string.indexOf("[");
int j = string.indexOf("]");
if (i > -1 && j > -1)
{
- UserColourScheme ucs = new UserColourScheme();
-
- colour = ucs.getColourFromString(string.substring(i + 1, j));
+ colour = ColorUtils.parseColourString(string.substring(i + 1,
+ j));
if (i > 0 && string.charAt(i - 1) == ',')
{
// clip the preceding comma as well
}
}
if (hasSymbols
- && (token.equals("H") || token.equals("E")
- || token.equals("S") || token.equals(" ")))
+ && (token.length() == 1 && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz"
+ .contains(token)))
{
// Either this character represents a helix or sheet
// or an integer which can be displayed
void colourAnnotations(AlignmentI al, String label, String colour)
{
- UserColourScheme ucs = new UserColourScheme(colour);
+ Color awtColour = ColorUtils.parseColourString(colour);
Annotation[] annotations;
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
{
{
if (annotations[j] != null)
{
- annotations[j].colour = ucs.findColour('A');
+ annotations[j].colour = awtColour;
}
}
}
SequenceGroup groupRef)
{
String group = st.nextToken();
- AlignmentAnnotation annotation = null, alannot[] = al
- .getAlignmentAnnotation();
- float value = new Float(st.nextToken()).floatValue();
+ AlignmentAnnotation[] alannot = al.getAlignmentAnnotation();
+ String nextToken = st.nextToken();
+ float value = 0f;
+ try
+ {
+ value = Float.valueOf(nextToken);
+ } catch (NumberFormatException e)
+ {
+ System.err.println("line " + nlinesread + ": Threshold '" + nextToken
+ + "' invalid, setting to zero");
+ }
String label = st.hasMoreTokens() ? st.nextToken() : null;
- java.awt.Color colour = null;
+ Color colour = null;
if (st.hasMoreTokens())
{
- UserColourScheme ucs = new UserColourScheme(st.nextToken());
- colour = ucs.findColour('A');
+ colour = ColorUtils.parseColourString(st.nextToken());
}
if (alannot != null)
{
}
}
}
- if (annotation == null)
- {
- return;
- }
}
void addGroup(AlignmentI al, StringTokenizer st)
if (sg != null)
{
String keyValue, key, value;
- ColourSchemeI def = sg.cs;
- sg.cs = null;
+ ColourSchemeI def = sg.getColourScheme();
while (st.hasMoreTokens())
{
keyValue = st.nextToken();
}
else if (key.equalsIgnoreCase("colour"))
{
- sg.cs = ColourSchemeProperty.getColour(al, value);
+ sg.cs.setColourScheme(ColourSchemeProperty
+ .getColourScheme(al, value));
}
else if (key.equalsIgnoreCase("pidThreshold"))
{
else if (key.equalsIgnoreCase("consThreshold"))
{
sg.cs.setConservationInc(Integer.parseInt(value));
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null),
+ Conservation c = new Conservation("Group", sg.getSequences(null),
sg.getStartRes(), sg.getEndRes() + 1);
c.calculate();
}
else if (key.equalsIgnoreCase("outlineColour"))
{
- sg.setOutlineColour(new UserColourScheme(value).findColour('A'));
+ sg.setOutlineColour(ColorUtils.parseColourString(value));
}
else if (key.equalsIgnoreCase("displayBoxes"))
{
}
else if (key.equalsIgnoreCase("textCol1"))
{
- sg.textColour = new UserColourScheme(value).findColour('A');
+ sg.textColour = ColorUtils.parseColourString(value);
}
else if (key.equalsIgnoreCase("textCol2"))
{
- sg.textColour2 = new UserColourScheme(value).findColour('A');
+ sg.textColour2 = ColorUtils.parseColourString(value);
}
else if (key.equalsIgnoreCase("textColThreshold"))
{
}
else if (key.equalsIgnoreCase("idColour"))
{
- // consider warning if colour doesn't resolve to a real colour
- sg.setIdColour((def = new UserColourScheme(value))
- .findColour('A'));
+ Color idColour = ColorUtils.parseColourString(value);
+ sg.setIdColour(idColour == null ? Color.black : idColour);
}
else if (key.equalsIgnoreCase("hide"))
{
}
sg.recalcConservation();
}
- if (sg.cs == null)
+ if (sg.getColourScheme() == null)
{
- sg.cs = def;
+ sg.setColourScheme(def);
}
}
}
*/
public String printCSVAnnotations(AlignmentAnnotation[] annotations)
{
+ if (annotations == null)
+ {
+ return "";
+ }
StringBuffer sp = new StringBuffer();
for (int i = 0; i < annotations.length; i++)
{
git://source.jalview.org / jalview.git / blobdiff