import jalview.analysis.AlignmentUtils;
import jalview.api.AlignmentViewPanel;
import jalview.bin.ArgParser.Arg;
-import jalview.bin.ArgParser.ArgValues;
-import jalview.bin.ArgParser.SubVal;
+import jalview.bin.ArgParser.ArgValue;
+import jalview.bin.ArgParser.ArgValuesMap;
+import jalview.bin.ArgParser.SubVals;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
protected void processUnlinked(String id)
{
- Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+ ArgValuesMap avm = new ArgValuesMap(argParser.linkedArgs(id));
processLinked(id);
}
protected void processLinked(String id)
{
- Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+ ArgValuesMap avm = new ArgValuesMap(argParser.linkedArgs(id));
/*
// script to execute after all loading is completed one way or another
FileFormatI format = null;
DataSourceType protocol = null;
*/
- if (ArgParser.getArgValues(m, Arg.OPEN) != null)
+ if (avm.hasValue(Arg.OPEN))
{
long progress = -1;
boolean first = true;
AlignFrame af;
- for (String openFile : ArgParser.getValues(m, Arg.OPEN))
+ for (ArgValue av : avm.getArgValueList(Arg.OPEN))
{
+ String openFile = av.getValue();
if (openFile == null)
continue;
// get kind of temperature factor annotation
StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
- if ((!ArgParser.getBoolean(m, Arg.NOTEMPFAC))
- && ArgParser.getArgValues(m, Arg.TEMPFAC) != null)
+ if ((!avm.getBoolean(Arg.NOTEMPFAC)) && avm.hasValue(Arg.TEMPFAC))
{
try
{
- tempfacType = StructureImportSettings.TFType.valueOf(ArgParser
- .getValue(m, Arg.TEMPFAC).toUpperCase(Locale.ROOT));
+ tempfacType = StructureImportSettings.TFType
+ .valueOf(avm.getArgValue(Arg.TEMPFAC).getValue()
+ .toUpperCase(Locale.ROOT));
Console.debug("Obtained Temperature Factor type of '"
+ tempfacType + "'");
} catch (IllegalArgumentException e)
format);
// wrap alignment?
- if (ArgParser.getBoolean(m, Arg.WRAP))
+ if (avm.getBoolean(Arg.WRAP))
{
af.getCurrentView().setWrapAlignment(true);
}
// colour aligment?
- if (ArgParser.hasValue(m, Arg.COLOUR))
+ if (avm.hasValue(Arg.COLOUR))
{
- af.changeColour_actionPerformed(
- ArgParser.getValue(m, Arg.COLOUR));
+ af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
}
// change alignment frame title
- if (ArgParser.getValue(m, Arg.TITLE) != null)
- af.setTitle(ArgParser.getValue(m, Arg.TITLE));
+ if (avm.hasValue(Arg.TITLE))
+ af.setTitle(avm.getValue(Arg.TITLE));
/* hacky approach to hiding the annotations */
// show secondary structure annotations?
- if (ArgParser.getBoolean(m, Arg.SSANNOTATION))
+ if (avm.getBoolean(Arg.SSANNOTATION))
{
// do this better (annotation types?)
AlignmentUtils.showOrHideSequenceAnnotations(
}
// show temperature factor annotations?
- if (ArgParser.getBoolean(m, Arg.NOTEMPFAC))
+ if (avm.getBoolean(Arg.NOTEMPFAC))
{
// do this better (annotation types?)
List<String> hideThese = new ArrayList<>();
if (showTemperatureFactor)
*/
{
- if (ArgParser.getValue(m, Arg.TEMPFAC_LABEL) != null)
+ if (avm.hasValue(Arg.TEMPFAC_LABEL))
{
AlignmentAnnotation aa = AlignmentUtils
.getFirstSequenceAnnotationOfType(
af.getCurrentView().getAlignment(),
AlignmentAnnotation.LINE_GRAPH);
- String label = ArgParser.getValue(m, Arg.TEMPFAC_LABEL);
+ String label = avm.getValue(Arg.TEMPFAC_LABEL);
if (aa != null)
{
aa.label = label;
}
// open the structure (from same PDB file or given PDBfile)
- if (!ArgParser.getBoolean(m, Arg.NOSTRUCTURE))
+ if (!avm.getBoolean(Arg.NOSTRUCTURE))
{
AlignFrame af = afMap.get(id);
- if (ArgParser.getArgValues(m, Arg.STRUCTURE) != null)
+ if (avm.hasValue(Arg.STRUCTURE))
{
- for (String val : ArgParser.getValues(m, Arg.STRUCTURE))
+ for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
{
- SubVal subId = new SubVal(val);
+ String val = av.getValue();
+ SubVals subId = new SubVals(val);
SequenceI seq = getSpecifiedSequence(af, subId);
if (seq == null)
{
continue;
}
File structureFile = null;
- if (subId.content != null && subId.content.length() != 0)
+ if (subId.getContent() != null
+ && subId.getContent().length() != 0)
{
- structureFile = new File(subId.content);
+ structureFile = new File(subId.getContent());
Console.debug("Using structure file (from argument) '"
+ structureFile.getAbsolutePath() + "'");
}
}
// load a pAE file if given
- if (ArgParser.getValues(m, Arg.PAEMATRIX) != null)
+ if (avm.hasValue(Arg.PAEMATRIX))
{
AlignFrame af = afMap.get(id);
if (af != null)
{
- for (String val : ArgParser.getValues(m, Arg.PAEMATRIX))
+ for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
{
- SubVal subVal = ArgParser.getSubVal(val);
- File paeFile = new File(subVal.content);
+ String val = av.getValue();
+ SubVals subVals = ArgParser.getSubVals(val);
+ File paeFile = new File(subVals.getContent());
String paePath = null;
try
{
Console.warn(
"Problem with the PAE file path: '" + paePath + "'");
}
- String structId = "structid".equals(subVal.keyName)
- ? subVal.keyValue
- : null;
- if (subVal.notSet())
+ String structId = subVals.get("structid");
+ if (subVals.notSet())
{
// take structid from pdbfilename
}
- if ("structfile".equals(subVal.keyName))
+ if (subVals.has("structfile"))
{
Console.info("***** Attaching paeFile '" + paePath + "' to "
- + subVal.keyName + "=" + subVal.keyValue);
+ + "structfile=" + subVals.get("structfile"));
EBIAlfaFold.addAlphaFoldPAEToStructure(
af.getCurrentView().getAlignment(), paeFile,
- subVal.index, subVal.keyValue, false);
+ subVals.getIndex(), subVals.get("structfile"), false);
}
- else if ("structid".equals(subVal.keyName))
+ else if (subVals.has("structid"))
{
Console.info("***** Attaching paeFile '" + paePath + "' to "
- + subVal.keyName + "=" + subVal.keyValue);
+ + "structid=" + subVals.get("structid"));
EBIAlfaFold.addAlphaFoldPAEToStructure(
af.getCurrentView().getAlignment(), paeFile,
- subVal.index, subVal.keyValue, true);
+ subVals.getIndex(), subVals.get("structid"), true);
}
else
{
Console.debug("***** Attaching paeFile '" + paePath
- + "' to sequence index " + subVal.index);
+ + "' to sequence index " + subVals.getIndex());
EBIAlfaFold.addAlphaFoldPAEToSequence(
af.getCurrentView().getAlignment(), paeFile,
- subVal.index, null);
+ subVals.getIndex(), null);
// required to readjust the height and position of the pAE
// annotation
}
}
}
- boolean doShading = ArgParser.getBoolean(m, Arg.TEMPFAC_SHADING);
+ boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
if (doShading)
{
AlignFrame af = afMap.get(id);
protected void processImages(String id)
{
- Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+ ArgValuesMap avm = new ArgValuesMap(argParser.linkedArgs(id));
AlignFrame af = afMap.get(id);
if (af == null)
return;
}
- if (ArgParser.getValues(m, Arg.IMAGE) != null)
+ if (avm.hasValue(Arg.IMAGE))
{
- for (String val : ArgParser.getValues(m, Arg.IMAGE))
+ for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
{
- SubVal subVal = new SubVal(val);
+ String val = av.getValue();
+ SubVals subVal = new SubVals(val);
String type = "png"; // default
- String fileName = subVal.content;
+ String fileName = subVal.getContent();
File file = new File(fileName);
- if ("type".equals(subVal.keyName))
+ if (subVal.has("type"))
{
- type = subVal.keyValue;
+ type = subVal.get("type");
}
else if (fileName != null)
{
}
}
- private SequenceI getSpecifiedSequence(AlignFrame af, SubVal subId)
+ private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
{
AlignmentI al = af.getCurrentView().getAlignment();
- if (-1 < subId.index && subId.index < al.getSequences().size())
+ if (-1 < subId.getIndex()
+ && subId.getIndex() < al.getSequences().size())
{
- return al.getSequenceAt(subId.index);
+ return al.getSequenceAt(subId.getIndex());
}
- else if ("id".equals(subId.keyName))
+ else if (subId.has("seqid"))
{
- return al.findName(subId.keyValue);
+ return al.findName(subId.get("seqid"));
}
return null;
}