JALVIEW_ANNOTATION
HIDE_INSERTIONS
-STRUCTMODEL FER_CAPAN_1-144 c4n58A_ c4n58A_.1.pdb c4n58A_.1.fasta 1 54 48 143 <b>PDB Header: </b>Hyrolase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Pectocin m2<br> <b>PDB Title: </b>Crystal structure of pectocin m2 at 1.86 amgtroms
-STRUCTMODEL FER_CAPAN_1-144 d1a70a_ d1a70a_.2.pdb d1a70a_.2.fasta 1 71 48 144 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL FER_CAPAN_1-144 d1offa_ d1offa_.3.pdb d1offa_.3.fasta 1 73 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL FER_CAPAN_1-144 d1frra_ d1frra_.4.pdb d1frra_.4.fasta 0.999 62 49 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL FER_CAPAN_1-144 d1pfda_ d1pfda_.5.pdb d1pfda_.5.fasta 0.999 70 48 143 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL FER_CAPAN_1-144 d1frda_ d1frda_.6.pdb d1frda_.6.fasta 0.999 50 48 143 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL FER_CAPAN_1-144 d1fxia_ d1fxia_.7.pdb d1fxia_.7.fasta 0.999 62 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL FER_CAPAN_1-144 d1gaqb_ d1gaqb_.8.pdb d1gaqb_.8.fasta 0.999 71 48 144 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL FER_CAPAN_1-144 d1iuea_ d1iuea_.9.pdb d1iuea_.9.fasta 0.999 48 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL FER_CAPAN_1-144 d1awda_ d1awda_.10.pdb d1awda_.10.fasta 0.999 68 50 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL FER_CAPAN_1-144 d1wria_ d1wria_.11.pdb d1wria_.11.fasta 0.999 59 49 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL FER_CAPAN_1-144 d1czpa_ d1czpa_.12.pdb d1czpa_.12.fasta 0.999 64 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL FER_CAPAN_1-144 d2cjoa_ d2cjoa_.13.pdb d2cjoa_.13.fasta 0.999 63 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL FER_CAPAN_1-144 d4fxca_ d4fxca_.14.pdb d4fxca_.14.fasta 0.999 64 48 142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
-STRUCTMODEL FER_CAPAN_1-144 c4itkA_ c4itkA_.15.pdb c4itkA_.15.fasta 0.999 57 50 142 <b>PDB Header: </b>Electron transport<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Apoferredoxin <br><b>PDB Title: </b>The structure of c.reinhardtii ferredoxin 2
-STRUCTMODEL FER_CAPAN_1-144 c1krhA_ c1krhA_.16.pdb c1krhA_.16.fasta 0.999 25 48 142 <b>PDB Header: </b>Oxidoreductase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Benzoate 1,2-deoxygenase reductase <br> <b>PDB Title: </b>X-ray structure of benzoate deoxygenate reductase
-STRUCTMODEL FER_CAPAN_1-144 d1krha3 d1krha3.17.pdb d1krha3.17.fasta 0.999 24 48 143 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins
-STRUCTMODEL FER_CAPAN_1-144 d1jq4a_ d1jq4a_.18.pdb d1jq4a_.18.fasta 0.999 29 47 138 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins
-STRUCTMODEL FER_CAPAN_1-144 c4wqmA_ c4wqmA_.19.pdb c4wqmA_.19.fasta 0.999 28 49 144 <b>PDB header: </b>Oxidoreductase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Toluene-4-monooxygenase electron transfer component<br><b>PDB Title: </b>Structure of the toluene 4-monooxygenase nah oxidoreductase t4mof,2 k270s k271s variant
-STRUCTMODEL FER_CAPAN_1-144 c2piaA_ c2piaA_.20.pdb c2piaA_.20.fasta 0.999 22 1 136 <b>PDB header: </b>Reductase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Phthalate deoxygenase reductase<br><b>PDB Title: </b>Phthalate deoxygenate reductase: a modular structure for2 electron transfer from pyridine nucleotides to [2fe-2s]
\ No newline at end of file
+HEADER_STRUCT_MODEL QUERY_SEQ TEMPLATE_SEQ MODEL_FILE MAPPING_FILE Confidence % I.D Aligned Range Other Information
+STRUCTMODEL FER_CAPAN_1-144 c4n58A_ c4n58A_.1.pdb c4n58A_.1.fasta 1 54 48-143 <b>PDB Header: </b>Hyrolase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Pectocin m2<br> <b>PDB Title: </b>Crystal structure of pectocin m2 at 1.86 amgtroms
+STRUCTMODEL FER_CAPAN_1-144 d1a70a_ d1a70a_.2.pdb d1a70a_.2.fasta 1 71 48-144 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL FER_CAPAN_1-144 d1offa_ d1offa_.3.pdb d1offa_.3.fasta 1 73 48-142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL FER_CAPAN_1-144 d1frra_ d1frra_.4.pdb d1frra_.4.fasta 0.999 62 49-142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL FER_CAPAN_1-144 d1pfda_ d1pfda_.5.pdb d1pfda_.5.fasta 0.999 70 48-143 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL FER_CAPAN_1-144 d1frda_ d1frda_.6.pdb d1frda_.6.fasta 0.999 50 48-143 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL FER_CAPAN_1-144 d1fxia_ d1fxia_.7.pdb d1fxia_.7.fasta 0.999 62 48-142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL FER_CAPAN_1-144 d1gaqb_ d1gaqb_.8.pdb d1gaqb_.8.fasta 0.999 71 48-144 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL FER_CAPAN_1-144 d1iuea_ d1iuea_.9.pdb d1iuea_.9.fasta 0.999 48 48-142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL FER_CAPAN_1-144 d1awda_ d1awda_.10.pdb d1awda_.10.fasta 0.999 68 50-142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL FER_CAPAN_1-144 d1wria_ d1wria_.11.pdb d1wria_.11.fasta 0.999 59 49-142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL FER_CAPAN_1-144 d1czpa_ d1czpa_.12.pdb d1czpa_.12.fasta 0.999 64 48-142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL FER_CAPAN_1-144 d2cjoa_ d2cjoa_.13.pdb d2cjoa_.13.fasta 0.999 63 48-142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL FER_CAPAN_1-144 d4fxca_ d4fxca_.14.pdb d4fxca_.14.fasta 0.999 64 48-142 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related
+STRUCTMODEL FER_CAPAN_1-144 c4itkA_ c4itkA_.15.pdb c4itkA_.15.fasta 0.999 57 50-142 <b>PDB Header: </b>Electron transport<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Apoferredoxin <br><b>PDB Title: </b>The structure of c.reinhardtii ferredoxin 2
+STRUCTMODEL FER_CAPAN_1-144 c1krhA_ c1krhA_.16.pdb c1krhA_.16.fasta 0.999 25 48-142 <b>PDB Header: </b>Oxidoreductase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Benzoate 1,2-deoxygenase reductase <br> <b>PDB Title: </b>X-ray structure of benzoate deoxygenate reductase
+STRUCTMODEL FER_CAPAN_1-144 d1krha3 d1krha3.17.pdb d1krha3.17.fasta 0.999 24 48-143 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins
+STRUCTMODEL FER_CAPAN_1-144 d1jq4a_ d1jq4a_.18.pdb d1jq4a_.18.fasta 0.999 29 47-138 <b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins
+STRUCTMODEL FER_CAPAN_1-144 c4wqmA_ c4wqmA_.19.pdb c4wqmA_.19.fasta 0.999 28 49-144 <b>PDB header: </b>Oxidoreductase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Toluene-4-monooxygenase electron transfer component<br><b>PDB Title: </b>Structure of the toluene 4-monooxygenase nah oxidoreductase t4mof,2 k270s k271s variant
+STRUCTMODEL FER_CAPAN_1-144 c2piaA_ c2piaA_.20.pdb c2piaA_.20.fasta 0.999 22 1-136 <b>PDB header: </b>Reductase<br><b>Chain: </b>A<br><b>PDB Molecule: </b>Phthalate deoxygenase reductase<br><b>PDB Title: </b>Phthalate deoxygenate reductase: a modular structure for2 electron transfer from pyridine nucleotides to [2fe-2s]
+
+
+5 test that exercises 54 cases
\ No newline at end of file
public class AnnotationFile
{
+ StringBuffer text;
+
+ SequenceI refSeq = null;
+
+ String refSeqId = null;
+
+ String[] StructModelHeader = null;
+
+ long nlinesread = 0;
+
+ String lastread = "";
+
+ /**
+ * used for resolving absolute references to resources relative to
+ * annotationFile location
+ */
+ String baseUri = "";
+
+ private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE",
+ STRUCTMODEL = "STRUCTMODEL",
+ HEADER_STRUCT_MODEL = "HEADER_STRUCT_MODEL";
+
public AnnotationFile()
{
init();
return newline;
}
- StringBuffer text;
private void init()
{
}
}
- SequenceI refSeq = null;
-
- String refSeqId = null;
public boolean annotateAlignmentView(AlignViewportI viewport,
String file, DataSourceType protocol)
return false;
}
- long nlinesread = 0;
-
- String lastread = "";
-
- /**
- * 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
modified = true;
continue;
}
- // else if (token.equalsIgnoreCase("VIEW_DEF"))
- // {
- // addOrSetView(al,st);
- // modified = true;
- // continue;
- // }
else if (token.equalsIgnoreCase("VIEW_SETREF"))
{
if (refSeq != null)
modified = true;
continue;
}
+ else if (token.equalsIgnoreCase(HEADER_STRUCT_MODEL))
+ {
+ int hSize = st.countTokens();
+ StructModelHeader = new String[hSize];
+ for (int x = 0; x < hSize; x++)
+ {
+ StructModelHeader[x] = st.nextToken();
+ }
+ continue;
+ }
else if (token.equalsIgnoreCase(STRUCTMODEL))
{
boolean failedtoadd = true;
- // expect
- // STRUCTMODEL <Query> <TemplateSeqId> <ModelFile> <FastaMappingFile>
- // <Confidence> <%.I.D>
- // <MatchStart> <MatchEnd> <Coverage> [<Other Information>]
+ // expects STRUCTMODEL <Query> <TemplateSeqId> <ModelFile>
+ // <FastaMappingFile>
String querySeqId = !st.hasMoreTokens() ? "" : st.nextToken();
SequenceI querySeq = al.findName(querySeqId);
if (st.hasMoreTokens()) {
}
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))
+ int tSize = st.countTokens() + 2;
+ String[] rowData = new String[tSize];
+ rowData[0] = querySeqId;
+ rowData[1] = refSeqId;
+ for (int x = 2; x < tSize; x++)
+ {
+ rowData[x] = st.nextToken();
+ }
+ if (processStructModel(al, querySeq, refSeq,
+ StructModelHeader, rowData, baseUri))
{
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 ");
+ .println("Need minimum of <Query> <TemplateSeqId> <ModelFile> <FastaMappingFile> as tab separated fields after"
+ + STRUCTMODEL);
} else {
modified = true;
}
}
/**
- * resolve a structural model and generate and add an alignment sequence for
- * it
+ * Resolve structural model to a reference sequence and register it to
+ * StructureSelectionManager
*
- * @param refSeq2
- * @param tempId
- * @param urlToModel
- * @param urlToPairwise
+ * @param al
+ * @param querySequence
+ * @param templateSeq
+ * @param structModelHeader
+ * @param structModelData
* @return true if model and sequence was added
*/
- private boolean add_structmodel(AlignmentI al, SequenceI querySequence,
+ static boolean processStructModel(AlignmentI al, SequenceI querySequence,
SequenceI templateSeq,
- String modelFile, String fastaFile, String aRange,
- String coverage, String confidence,
- String pid, String otherInfo)
+ String[] structModelHeader,
+ String[] structModelData, String baseUri)
{
String warningMessage = null;
boolean added = false;
try {
- String structureModelFile = resolveAbsolute(modelFile);
- String fastaMappingFile = resolveAbsolute(fastaFile.replaceAll(
- ".fasta.jal", ".fasta"));
+ String structureModelFile = resolveAbsolutePath(structModelData[2],
+ baseUri);
+ String fastaMappingFile = resolveAbsolutePath(structModelData[3],
+ baseUri);
// System.out.println("Model File >> " + structureModelFile);
// System.out.println("Fasta File >> " + fastaMappingFile);
- PDBEntry phyre2PDBEntry = new PDBEntry(modelFile, null, Type.FILE,
+ String modelName = StructureFile.safeName(structureModelFile);
+ PDBEntry phyre2PDBEntry = new PDBEntry(modelName, " ",
+ Type.PDB,
structureModelFile);
- String phyre2ModelDesc = generatePhyre2InfoHTMLTable(aRange,
- coverage, confidence, pid, otherInfo);
+ String phyre2ModelDesc = generatePhyre2InfoHTMLTable(
+ structModelHeader, structModelData);
phyre2PDBEntry.setProperty("PHYRE2_MODEL_INFO", phyre2ModelDesc);
templateSeq.getDatasetSequence().addPDBId(phyre2PDBEntry);
if (querySequence != null)
return added;
}
- private String generatePhyre2InfoHTMLTable(String aRange,
- String coverage, String confidence, String pid, String otherInfo)
+ static String generatePhyre2InfoHTMLTable(String[] structModelHeader,
+ String[] structModelData)
{
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())
+ if (isGenerateStructInfoHtml(structModelHeader, structModelData))
{
- 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>");
+ phyre2InfoBuilder.append("<html><table border=\"1\" width=100%>")
+ .append("<tr><td colspan=\"2\"><strong>Phyre2 Template Info</strong></td></tr>");
+ for (int x = 4; x < structModelData.length; x++)
+ {
+ phyre2InfoBuilder.append("<tr><td>").append(structModelHeader[x])
+ .append("</td><td>").append(structModelData[x])
+ .append("</td></tr>");
+ }
+ phyre2InfoBuilder.append("</table></html>");
}
- if (pid != null && !pid.isEmpty())
+ return phyre2InfoBuilder.toString();
+ }
+
+ static boolean isGenerateStructInfoHtml(String[] header, String[] data)
+ {
+ boolean generate = true;
+ if (header == null || data == null)
{
- phyre2InfoBuilder.append("<tr><td>").append("%.i.d")
- .append("</td><td>").append(pid).append("</td></tr>");
+ return false;
}
- if (otherInfo != null && !otherInfo.isEmpty())
+ if (header.length < 3 || data.length < 3)
{
- phyre2InfoBuilder.append("<tr><td>").append("Other information")
- .append("</td><td>").append(otherInfo).append("</td></tr>");
+ generate = false;
}
- phyre2InfoBuilder.append("</table></html>");
- return phyre2InfoBuilder.toString();
+ return generate;
}
- private String resolveAbsolute(String relURI)
+ static String resolveAbsolutePath(String relURI, String _baseUri)
{
if (relURI.indexOf(":/") > -1 || relURI.startsWith("/")
- || "".equals(baseUri) || relURI.startsWith(baseUri))
+ || "".equals(_baseUri) || relURI.startsWith(_baseUri))
{
return relURI;
}
- return baseUri + relURI;
+ return _baseUri + relURI;
}
private void parseHideCols(ColumnSelection colSel, String nextToken)
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.io.AnnotationFile.ViewDef;
+import jalview.structure.StructureSelectionManager;
import java.io.File;
import java.util.Hashtable;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
public class AnnotationFileIOTest
{
+ private StructureSelectionManager ssm = null;
+
+ private AlignmentI al = null;
+
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
* - label for IO class used to write and read back in the data from
* f
*/
- void testAnnotationFileIO(String testname, File f,
- File annotFile)
+ void testAnnotationFileIO(String testname, File f, File annotFile)
{
System.out.println("Test: " + testname + "\nReading annotation file '"
+ annotFile + "' onto : " + f);
+ "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
+ annotFile + "'.");
}
+
+
+ @BeforeClass(alwaysRun = true)
+ void testProcessStructModel()
+ {
+ File alignmentFile = new File(
+ "examples/testdata/phyre2results/56da5616b4559c93/allhits.fasta");
+ String annotationFile = "examples/testdata/phyre2results/56da5616b4559c93/allhits.ann";
+ ColumnSelection cs = new ColumnSelection();
+ al = readAlignmentFile(alignmentFile);
+ boolean annotationRead = new AnnotationFile().readAnnotationFile(al,
+ cs, annotationFile, DataSourceType.FILE);
+ Assert.assertTrue(annotationRead);
+ ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ System.out.println("bla");
+ }
+
+ @Test(
+ groups = { "Functional" },
+ dataProvider = "phyre2ModelPDBEntryDataProvider")
+ void testSequence_PDBEntryAssociation(String[] structModelHeader, String baseDir,
+ String structModelDataStr)
+ {
+ String structModelData[] = structModelDataStr.split("\t");
+ String templateSeq = structModelData[1];
+ String pdbId = structModelData[2];
+
+ SequenceI testSeq = al.findName(templateSeq);
+ Assert.assertNotNull(testSeq);
+ PDBEntry actualPDBEntry = testSeq.getDatasetSequence().getPDBEntry(
+ pdbId);
+ Assert.assertNotNull(actualPDBEntry);
+
+ PDBEntry expectedPDBEntry = new PDBEntry(pdbId, " ", Type.PDB, baseDir
+ + pdbId);
+ String phyre2ModelDesc = AnnotationFile.generatePhyre2InfoHTMLTable(structModelHeader,
+ structModelData);
+ expectedPDBEntry.setProperty("PHYRE2_MODEL_INFO", phyre2ModelDesc);
+ Assert.assertEquals(actualPDBEntry, expectedPDBEntry);
+ }
+
+ @Test(
+ groups = { "Functional" },
+ dataProvider = "phyre2ModelMappingDataProvider")
+ void testPhyre2ModelRegistration(String phyre2ModelFile,
+ String expectedPhyre2FastaMappingFile)
+ {
+
+ String actualFastaMappingFile = ssm
+ .getPhyre2FastaFileFor(phyre2ModelFile);
+ Assert.assertNotNull(actualFastaMappingFile);
+ Assert.assertEquals(actualFastaMappingFile,
+ expectedPhyre2FastaMappingFile);
+ }
+
+ @Test(
+ groups = { "Functional" },
+ dataProvider = "phyre2InfoHTMLTableDataProvider")
+ void testGeneratePhyre2InfoHTMLTable(String caseDescription,
+ String[] header, String[] data, String expectedHtml)
+ {
+ System.out.println(">>>> Testing Case - " + caseDescription);
+ String actualHtmlGenerated = AnnotationFile
+ .generatePhyre2InfoHTMLTable(header, data);
+ System.out.println("-----> " + actualHtmlGenerated);
+ Assert.assertEquals(actualHtmlGenerated, expectedHtml);
+ }
+
+ @Test(
+ groups = { "Functional" },
+ dataProvider = "StructModelHtmlDataProvider")
+ void testIsGenerateStructInfoHtml(String caseDescription,
+ String[] header, String[] data, boolean expectedOutcome)
+ {
+ System.out.println(">>>> Testing Case - " + caseDescription);
+ boolean actual = AnnotationFile.isGenerateStructInfoHtml(header, data);
+ Assert.assertEquals(actual, expectedOutcome);
+ }
+
+ @Test(groups = { "Functional" }, dataProvider = "FilePathProvider")
+ void testResolveAbsolutePath(String caseDescription, String suppliedPath,
+ String baseURI, String expectedURI)
+ {
+ System.out.println(">>>> Testing Case - " + caseDescription);
+ String actualURI = AnnotationFile.resolveAbsolutePath(suppliedPath,
+ baseURI);
+ Assert.assertEquals(actualURI, expectedURI);
+ }
+
+ @DataProvider(name = "phyre2ModelPDBEntryDataProvider")
+ public static Object[][] phyre2ModelPDBEntryDataProvider()
+ {
+ String[] structModelHeader = new String[] { "QUERY_SEQ",
+ "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE", "Confidence",
+ "% I.D", "Aligned Range", "Other Information"};
+ String baseDir = "examples/testdata/phyre2results/56da5616b4559c93/";
+
+ return new Object[][] {
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\tc4n58A_\tc4n58A_.1.pdb\tc4n58A_.1.fasta\t1\t54\t48-143\t<b>PDB Header: </b>Hyrolase<br><b>Chain: "
+ + "</b>A<br><b>PDB Molecule: </b>Pectocin m2<br> <b>PDB Title: </b>Crystal structure of pectocin m2 at 1.86 amgtroms" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\td1a70a_\td1a70a_.2.pdb\td1a70a_.2.fasta\t1\t71\t48-144\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
+ + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\td1offa_\td1offa_.3.pdb\td1offa_.3.fasta\t1\t73\t48-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
+ + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\td1frra_\td1frra_.4.pdb\td1frra_.4.fasta\t0.999\t62\t49-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
+ + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\td1pfda_\td1pfda_.5.pdb\td1pfda_.5.fasta\t0.999\t70\t48-143\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
+ + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\td1frda_\td1frda_.6.pdb\td1frda_.6.fasta\t0.999\t50\t48-143\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
+ + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\td1fxia_\td1fxia_.7.pdb\td1fxia_.7.fasta\t0.999\t62\t48-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
+ + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\td1gaqb_\td1gaqb_.8.pdb\td1gaqb_.8.fasta\t0.999\t71\t48-144\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
+ + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\td1iuea_\td1iuea_.9.pdb\td1iuea_.9.fasta\t0.999\t48\t48-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
+ + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\td1awda_\td1awda_.10.pdb\td1awda_.10.fasta\t0.999\t68\t50-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
+ + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\td1wria_\td1wria_.11.pdb\td1wria_.11.fasta\t0.999\t59\t49-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
+ + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\td1czpa_\td1czpa_.12.pdb\td1czpa_.12.fasta\t0.999\t64\t48-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
+ + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\td2cjoa_\td2cjoa_.13.pdb\td2cjoa_.13.fasta\t0.999\t63\t48-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
+ + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\td4fxca_\td4fxca_.14.pdb\td4fxca_.14.fasta\t0.999\t64\t48-142\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
+ + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\tc4itkA_\tc4itkA_.15.pdb\tc4itkA_.15.fasta\t0.999\t57\t50-142\t<b>PDB Header: </b>Electron transport<br>"
+ + "<b>Chain: </b>A<br><b>PDB Molecule: </b>Apoferredoxin <br><b>PDB Title: </b>The structure of c.reinhardtii ferredoxin 2" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\tc1krhA_\tc1krhA_.16.pdb\tc1krhA_.16.fasta\t0.999\t25\t48-142\t<b>PDB Header: </b>Oxidoreductase<br><b>Chain: "
+ + "</b>A<br><b>PDB Molecule: </b>Benzoate 1,2-deoxygenase reductase <br> <b>PDB Title: </b>X-ray structure of benzoate "
+ + "deoxygenate reductase" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\td1krha3\td1krha3.17.pdb\td1krha3.17.fasta\t0.999\t24\t48-143\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
+ + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\td1jq4a_\td1jq4a_.18.pdb\td1jq4a_.18.fasta\t0.999\t29\t47-138\t<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br>"
+ + "<b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin domains from multi domain proteins" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\tc4wqmA_\tc4wqmA_.19.pdb\tc4wqmA_.19.fasta\t0.999\t28\t49-144\t<b>PDB header: </b>Oxidoreductase<br><b>Chain: "
+ + "</b>A<br><b>PDB Molecule: </b>Toluene-4-monooxygenase electron transfer component<br><b>PDB Title: </b>Structure of the "
+ + "toluene 4-monooxygenase nah oxidoreductase t4mof,2 k270s k271s variant" },
+ {
+ structModelHeader,
+ baseDir,
+ "FER_CAPAN_1-144\tc2piaA_\tc2piaA_.20.pdb\tc2piaA_.20.fasta\t0.999\t22\t1-136\t<b>PDB header: </b>Reductase<br><b>Chain: "
+ + "</b>A<br><b>PDB Molecule: </b>Phthalate deoxygenase reductase<br><b>PDB Title: </b>Phthalate deoxygenate reductase: a"
+ + " modular structure for2 electron transfer from pyridine nucleotides to [2fe-2s]" }
+ };
+ }
+
+ @DataProvider(name = "phyre2ModelMappingDataProvider")
+ public static Object[][] phyre2ModelMappingDataProvider()
+ {
+ return new Object[][] {
+
+ { "examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/c4n58A_.1.fasta" },
+ { "examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/d1a70a_.2.fasta" },
+ { "examples/testdata/phyre2results/56da5616b4559c93/d1offa_.3.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/d1offa_.3.fasta" },
+ { "examples/testdata/phyre2results/56da5616b4559c93/d1frra_.4.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/d1frra_.4.fasta" },
+ { "examples/testdata/phyre2results/56da5616b4559c93/d1pfda_.5.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/d1pfda_.5.fasta" },
+ { "examples/testdata/phyre2results/56da5616b4559c93/d1frda_.6.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/d1frda_.6.fasta" },
+
+ { "examples/testdata/phyre2results/56da5616b4559c93/d1fxia_.7.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/d1fxia_.7.fasta" },
+
+ { "examples/testdata/phyre2results/56da5616b4559c93/d1gaqb_.8.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/d1gaqb_.8.fasta" },
+ { "examples/testdata/phyre2results/56da5616b4559c93/d1iuea_.9.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/d1iuea_.9.fasta" },
+ {
+ "examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/d1awda_.10.fasta" },
+ {
+ "examples/testdata/phyre2results/56da5616b4559c93/d1wria_.11.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/d1wria_.11.fasta" },
+ {
+ "examples/testdata/phyre2results/56da5616b4559c93/d1czpa_.12.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/d1czpa_.12.fasta" },
+ {
+ "examples/testdata/phyre2results/56da5616b4559c93/d2cjoa_.13.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/d2cjoa_.13.fasta" },
+ {
+ "examples/testdata/phyre2results/56da5616b4559c93/d4fxca_.14.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/d4fxca_.14.fasta" },
+ {
+ "examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/c4itkA_.15.fasta" },
+ {
+ "examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.16.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/c1krhA_.16.fasta" },
+ {
+ "examples/testdata/phyre2results/56da5616b4559c93/d1krha3.17.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/d1krha3.17.fasta" },
+ {
+ "examples/testdata/phyre2results/56da5616b4559c93/d1jq4a_.18.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/d1jq4a_.18.fasta" },
+ {
+ "examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/c4wqmA_.19.fasta" },
+ {
+ "examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.pdb",
+ "examples/testdata/phyre2results/56da5616b4559c93/c2piaA_.20.fasta" }
+
+ };
+ }
+
+ @DataProvider(name = "phyre2InfoHTMLTableDataProvider")
+ public static Object[][] phyre2InfoHTMLTableDataProvider()
+ {
+ return new Object[][] {
+ {
+ "STRUCTMODEL Annotation with no headear information provided",
+ null,
+ new String[] { "FER_CAPAN_1-144", "d1a70a_ d1a70a_.2.pdb",
+ "d1a70a_.2.fasta", }, "" },
+ {
+ "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
+ new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
+ "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE" },
+ new String[] { "FER_CAPAN_1-144", "d1a70a_ d1a70a_.2.pdb",
+ "d1a70a_.2.fasta", },
+ "<html><table border=\"1\" width=100%><tr><td colspan=\"2\"><strong>Phyre2 Template Info</strong></td></tr></table></html>" },
+ {
+ "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
+ new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
+ "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE", "Confidence",
+ "% I.D", "Aligned Range", "Other Information", "Coverage" },
+ new String[] {
+ "FER_CAPAN_1-144",
+ "d1a70a_ d1a70a_.2.pdb",
+ "d1a70a_.2.fasta",
+ "1",
+ "71",
+ "48-144",
+ "<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
+ "<html><table border=\"1\" width=100%><tr><td colspan=\"2\"><strong>Phyre2 Template Info</strong></td></tr><tr><td>MAPPING_FILE</td><td>71</td></tr><tr><td>Confidence</td><td>48-144</td></tr><tr><td>% I.D</td><td><b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related</td></tr></table></html>" } };
+ }
+
+ @DataProvider(name = "StructModelHtmlDataProvider")
+ public static Object[][] IsGenerateStructInfoHtmlDataProvider()
+ {
+ return new Object[][] {
+ { "STRUCTMODEL Annotation with no headear or data provided", null,
+ null, false },
+ {
+ "STRUCTMODEL Annotation with headear information and no data column provided",
+ new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ" }, null,
+ false },
+ {
+ "STRUCTMODEL Annotation with no headear information provided",
+ null,
+ new String[] { "FER_CAPAN_1-144", "d1a70a_ d1a70a_.2.pdb",
+ "d1a70a_.2.fasta", }, false },
+ {
+ "STRUCTMODEL Annotation with only two headear information and two data column provided",
+ new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ" },
+ new String[] { "FER_CAPAN_1-144", "d1a70a_" }, false },
+ {
+ "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
+ new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
+ "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE" },
+ new String[] { "FER_CAPAN_1-144", "d1a70a_", "d1a70a_.2.pdb",
+ "d1a70a_.2.fasta", }, true },
+ {
+ "STRUCTMODEL Annotation with complete compulsary data and headear information provided",
+ new String[] { "HEADER_STRUCT_MODEL", "QUERY_SEQ",
+ "TEMPLATE_SEQ", "MODEL_FILE", "MAPPING_FILE", "Confidence",
+ "% I.D", "Aligned Range", "Other Information", "Coverage" },
+ new String[] {
+ "FER_CAPAN_1-144",
+ "d1a70a_",
+ "d1a70a_.2.pdb",
+ "d1a70a_.2.fasta",
+ "1",
+ "71",
+ "48-144",
+ "<b>Fold: </b>Beta-Grasp (ubiquitin-like)<br><b>Superfamily: </b>2Fe-2S ferredoxin-like<br><b>Family: </b>2Fe-2S ferredoxin-related" },
+ true } };
+ }
+
+ @DataProvider(name = "FilePathProvider")
+ public static Object[][] filePathProvider()
+ {
+ return new Object[][] {
+ { "relative local file path resolution", "c4n58A_.1.pdb", "",
+ "c4n58A_.1.pdb" },
+ { "relative local file path resolution", "c4n58A_.1.pdb",
+ "/examples/testdata/phyre2results/",
+ "/examples/testdata/phyre2results/c4n58A_.1.pdb" },
+ {
+ "relative URL path resolution",
+ "c4n58A_.1.pdb",
+ "http://www.jalview.org/builds/develop/examples/testdata/phyre2results/",
+ "http://www.jalview.org/builds/develop/examples/testdata/phyre2results/c4n58A_.1.pdb" },
+ {
+ "Absolute local file path resolution",
+ "/examples/testdata/phyre2results_xx/c4n58A_.1.pdb",
+ "/examples/testdata/phyre2results/",
+ "/examples/testdata/phyre2results_xx/c4n58A_.1.pdb" },
+ {
+ "Absolute URL path resolution",
+ "http://www.jalview.org/builds/develop/another_directory/c4n58A_.1.pdb",
+ "http://www.jalview.org/builds/develop/examples/testdata/phyre2results/",
+ "http://www.jalview.org/builds/develop/another_directory/c4n58A_.1.pdb" } };
+ }
}
git://source.jalview.org / jalview.git / commitdiff