import java.util.Map.Entry;
import jalview.analysis.AlignmentUtils;
-import jalview.api.AlignmentViewPanel;
import jalview.bin.argparser.Arg;
import jalview.bin.argparser.ArgParser;
import jalview.bin.argparser.ArgValue;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
import jalview.schemes.AnnotationColourGradient;
-import jalview.structure.StructureImportSettings;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.ws.dbsources.EBIAlfaFold;
import mc_view.PDBChain;
public class Commands
* ssm.setProcessSecondaryStructure(showSecondaryStructure); }
*/
- // get kind of temperature factor annotation
- StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
- if ((!avm.getBoolean(Arg.NOTEMPFAC))
- && avm.containsArg(Arg.TEMPFAC))
- {
- try
- {
- tempfacType = StructureImportSettings.TFType
- .valueOf(avm.getArgValue(Arg.TEMPFAC).getValue()
- .toUpperCase(Locale.ROOT));
- Console.debug("Obtained Temperature Factor type of '"
- + tempfacType + "'");
- } catch (IllegalArgumentException e)
- {
- // Just an error message!
- StringBuilder sb = new StringBuilder().append("Cannot set ")
- .append(Arg.TEMPFAC.argString()).append(" to '")
- .append(tempfacType)
- .append("', ignoring. Valid values are: ");
- Iterator<StructureImportSettings.TFType> it = Arrays
- .stream(StructureImportSettings.TFType.values())
- .iterator();
- while (it.hasNext())
- {
- sb.append(it.next().toString().toLowerCase(Locale.ROOT));
- if (it.hasNext())
- sb.append(", ");
- }
- Console.warn(sb.toString());
- }
- }
-
Console.debug(
"Opening '" + openFile + "' in new alignment frame");
FileLoader fileLoader = new FileLoader(!headless);
- StructureImportSettings.setTemperatureFactorType(tempfacType);
-
af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
format);
for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
{
String val = av.getValue();
- SubVals subId = new SubVals(val);
- SequenceI seq = getSpecifiedSequence(af, subId);
+ SubVals subVals = av.getSubVals();
+ SequenceI seq = getSpecifiedSequence(af, subVals);
if (seq == null)
{
// Could not find sequence from subId, let's assume the first
continue;
}
File structureFile = null;
- if (subId.getContent() != null
- && subId.getContent().length() != 0)
+ if (subVals.getContent() != null
+ && subVals.getContent().length() != 0)
{
- structureFile = new File(subId.getContent());
+ structureFile = new File(subVals.getContent());
Console.debug("Using structure file (from argument) '"
+ structureFile.getAbsolutePath() + "'");
}
StructureViewer.ViewerType.JMOL.toString());
}
- // get tft, paeFilename, label?
- /*
- * ArgValue tftAv = avm.getArgValuesReferringTo("structid", structId,
- * Arg.TEMPFAC);
- */
- StructureChooser.openStructureFileForSequence(null, null, ap, seq,
- false, structureFile.getAbsolutePath(), null, null); // tft,
- // paeFilename);
- }
- }
- }
+ String structureFilepath = structureFile.getAbsolutePath();
- // load a PAE file if given
- if (avm.containsArg(Arg.PAEMATRIX))
- {
- AlignFrame af = afMap.get(id);
- if (af != null)
- {
- for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
- {
- String val = av.getValue();
- SubVals subVals = ArgParser.getSubVals(val);
- String paeLabel = subVals.get("label");
- File paeFile = new File(subVals.getContent());
- String paePath = null;
- try
+ // get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
+ String paeFilepath = subVals.getWithSubstitutions(argParser, id,
+ "paematrix");
+ String paeLabel = subVals.get("paelabel");
+ ArgValue paeAv = getArgAssociatedWithStructure(Arg.PAEMATRIX, avm,
+ af, structureFilepath);
+ if (paeFilepath == null && paeAv != null)
{
- paePath = paeFile.getCanonicalPath();
- } catch (IOException e)
+ SubVals sv = paeAv.getSubVals();
+ File paeFile = new File(sv.getContent());
+
+ paeLabel = sv.get("label");
+ try
+ {
+ paeFilepath = paeFile.getCanonicalPath();
+ } catch (IOException e)
+ {
+ paeFilepath = paeFile.getAbsolutePath();
+ Console.warn("Problem with the PAE file path: '"
+ + paeFile.getPath() + "'");
+ }
+ }
+
+ // get TEMPFAC type from subvals or Arg.TEMPFAC
+ String tftString = subVals.get("tempfac");
+ TFType tft = avm.getBoolean(Arg.NOTEMPFAC) ? null
+ : TFType.DEFAULT;
+ ArgValue tftAv = getArgAssociatedWithStructure(Arg.TEMPFAC, avm,
+ af, structureFilepath);
+ if (tftString == null && tftAv != null)
{
- paePath = paeFile.getAbsolutePath();
- Console.warn(
- "Problem with the PAE file path: '" + paePath + "'");
+ tftString = tftAv.getSubVals().getContent();
}
- String structid = null;
- String structfile = null;
- int seqindex = SubVals.NOTSET;
- if (subVals.notSet())
+ if (tftString != null)
{
- ArgValue likelyStructure = avm
- .getClosestPreviousArgValueOfArg(av, Arg.STRUCTURE);
- if (likelyStructure != null)
+ // get kind of temperature factor annotation
+ try
{
- SubVals sv = likelyStructure.getSubVals();
- if (sv != null && sv.has(ArgValues.ID))
- {
- structid = sv.get(ArgValues.ID);
- }
- else
+ tft = TFType.valueOf(tftString.toUpperCase(Locale.ROOT));
+ Console.debug("Obtained Temperature Factor type of '" + tft
+ + "' for structure '" + structureFilepath + "'");
+ } catch (IllegalArgumentException e)
+ {
+ // Just an error message!
+ StringBuilder sb = new StringBuilder().append("Cannot set ")
+ .append(Arg.TEMPFAC.argString()).append(" to '")
+ .append(tft)
+ .append("', ignoring. Valid values are: ");
+ Iterator<TFType> it = Arrays.stream(TFType.values())
+ .iterator();
+ while (it.hasNext())
{
- structfile = likelyStructure.getValue();
- Console.debug(
- "##### Using closest previous structure argument '"
- + structfile + "'");
+ sb.append(it.next().toString().toLowerCase(Locale.ROOT));
+ if (it.hasNext())
+ sb.append(", ");
}
+ Console.warn(sb.toString());
}
}
- else if (subVals.has("structfile"))
- {
- structfile = subVals.get("structfile");
- }
- else if (subVals.has("structid"))
- {
- structid = subVals.get("structid");
- }
- if (structfile != null)
- {
- Console.info("##### Attaching paeFile '" + paePath + "' to "
- + "structfile=" + structfile);
- EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, seqindex, structfile, true, false, paeLabel);
- }
- else if (structid != null)
- {
- Console.info("##### Attaching paeFile '" + paePath + "' to "
- + "structid=" + structid);
- EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, seqindex, subVals.get("structid"), true, true,
- paeLabel);
- }
- else
- {
- seqindex = subVals.getIndex();
- Console.debug("##### Attaching paeFile '" + paePath
- + "' to sequence index " + seqindex);
- EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, seqindex, null, false, false, paeLabel);
- // required to readjust the height and position of the PAE
- // annotation
- }
- for (AlignmentViewPanel ap : af.getAlignPanels())
- {
- ap.adjustAnnotationHeight();
- }
+
+ // TODO pass PAE label
+ StructureChooser.openStructureFileForSequence(null, null, ap, seq,
+ false, structureFilepath, tft, paeFilepath);
}
}
}
for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
{
String val = av.getValue();
- SubVals subVal = new SubVals(val);
+ SubVals subVal = av.getSubVals();
String type = "png"; // default
String fileName = subVal.getContent();
File file = new File(fileName);
}
return null;
}
+
+ // returns the first Arg value intended for the structure structFilename
+ // (in the given AlignFrame from the ArgValuesMap)
+ private ArgValue getArgAssociatedWithStructure(Arg arg, ArgValuesMap avm,
+ AlignFrame af, String structFilename)
+ {
+ if (af != null)
+ {
+ for (ArgValue av : avm.getArgValueList(arg))
+ {
+ SubVals subVals = av.getSubVals();
+ String structid = subVals.get("structid");
+ String structfile = subVals.get("structfile");
+
+ // let's find a structure
+ if (structfile == null && structid == null)
+ {
+ ArgValue likelyStructure = avm.getClosestPreviousArgValueOfArg(av,
+ Arg.STRUCTURE);
+ if (likelyStructure != null)
+ {
+ SubVals sv = likelyStructure.getSubVals();
+ if (sv != null && sv.has(ArgValues.ID))
+ {
+ structid = sv.get(ArgValues.ID);
+ }
+ else
+ {
+ structfile = likelyStructure.getValue();
+ Console.debug(
+ "##### Comparing closest previous structure argument '"
+ + structfile + "'");
+ }
+ }
+ }
+
+ if (structfile == null && structid != null)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ if (ssm != null)
+ {
+ structfile = ssm.findFileForPDBId(structid);
+ }
+ }
+ if (structfile != null && structfile.equals(structFilename))
+ {
+ return av;
+ }
+ }
+ }
+ return null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff