package jalview.bin;
import java.io.File;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
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;
import jalview.io.FileLoader;
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
{
private Map<String, AlignFrame> afMap;
- public static void processArgs(ArgParser ap, boolean h)
+ public static boolean processArgs(ArgParser ap, boolean h)
{
argParser = ap;
headless = h;
+ boolean argsWereParsed = false;
+ if (headless)
+ {
+ System.setProperty("java.awt.headless", "true");
+ }
+
if (argParser != null && argParser.linkedIds() != null)
{
for (String id : argParser.linkedIds())
cmds.processLinked(id);
}
cmds.processImages(id);
+ argsWereParsed |= cmds.wereParsed();
}
- if (argParser.getBool(Arg.QUIT))
- {
- Jalview.getInstance().quit();
- }
}
+ if (argParser.getBool(Arg.QUIT))
+ {
+ Jalview.getInstance().quit();
+ return true;
+ }
+ // carry on with jalview.bin.Jalview
+ return argsWereParsed;
+ }
+
+ boolean argsWereParsed = false;
+
+ private boolean wereParsed()
+ {
+ return argsWereParsed;
}
public Commands()
protected void processUnlinked(String 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;
- OPEN: for (String openFile : ArgParser.getValues(m, Arg.OPEN))
+ for (ArgValue av : avm.getArgValueList(Arg.OPEN))
{
+ String openFile = av.getValue();
if (openFile == null)
- continue OPEN;
+ continue;
+ argsWereParsed = true;
if (first)
{
first = false;
if (!(new File(openFile)).exists())
{
Console.warn("Can't find file '" + openFile + "'");
- continue OPEN;
}
}
}
// 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 (avm.hasValue(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;
// store the AlignFrame for this id
afMap.put(id, af);
+
+ // is it its own structure file?
+ if (format.isStructureFile())
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
+ ssm.computeMapping(false, new SequenceI[] { seq }, null,
+ openFile, DataSourceType.FILE, null);
+ }
}
else
{
af.getCurrentView().addFile(new File(openFile), format);
}
- System.out
- .println("Command " + Arg.OPEN + " executed successfully!");
+ Console.debug("Command " + Arg.OPEN + " executed successfully!");
}
if (first) // first=true means nothing opened
Console.error("Could not open any files in headless mode");
System.exit(1);
}
- }
- else
- {
- Console.warn("No more files to open");
- if (desktop != null)
- desktop.setProgressBar(null, progress);
- }
-
- }
-
- // load a pAE file if given
- if (ArgParser.getValues(m, Arg.PAEMATRIX) != null)
- {
- AlignFrame af = afMap.get(id);
- if (af != null)
- {
- for (String val : ArgParser.getValues(m, Arg.PAEMATRIX))
+ else
{
- SubVal subVal = ArgParser.getSubVal(val);
- File paeFile = new File(subVal.content);
- if ("structid".equals(subVal.index))
- {
- EBIAlfaFold.addAlphaFoldPAEToStructure(
- af.getCurrentView().getAlignment(), paeFile,
- subVal.index, subVal.keyValue);
- }
- else
- {
- EBIAlfaFold.addAlphaFoldPAEToSequence(af.getCurrentView().getAlignment(),
- paeFile, subVal.index,
- "id".equals(subVal.keyName) ? subVal.keyValue : null);
- // required to readjust the height and position of the pAE
- // annotation
- }
- for (AlignmentViewPanel ap : af.getAlignPanels())
- {
- ap.adjustAnnotationHeight();
- }
+ Console.warn("No more files to open");
+ if (desktop != null)
+ desktop.setProgressBar(null, progress);
}
}
+
}
// 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))
{
- 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)
{
Console.warn("Could not find sequence for argument --"
+ Arg.STRUCTURE + "=" + val);
- break STRUCTURE;
+ // you probably want to continue here, not break
+ // break;
+ 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() + "'");
}
+
+ // TRY THIS
+ /*
+ PDBEntry fileEntry = new AssociatePdbFileWithSeq()
+ .associatePdbWithSeq(selectedPdbFileName,
+ DataSourceType.FILE, selectedSequence, true,
+ Desktop.instance);
+
+ sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry },
+ ap, new SequenceI[]
+ { selectedSequence });
+
+ */
+
/* THIS DOESN'T WORK */
else if (seq.getAllPDBEntries() != null
&& seq.getAllPDBEntries().size() > 0)
if (structureFile == null)
{
Console.warn("Not provided structure file with '" + val + "'");
- continue STRUCTURE;
+ continue;
}
if (!structureFile.exists())
{
Console.warn("Structure file '"
+ structureFile.getAbsoluteFile() + "' not found.");
- continue STRUCTURE;
+ continue;
}
Console.debug("Using structure file "
}
}
}
+
+ // load a pAE file if given
+ if (avm.hasValue(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);
+ File paeFile = new File(subVals.getContent());
+ String paePath = null;
+ try
+ {
+ paePath = paeFile.getCanonicalPath();
+ } catch (IOException e)
+ {
+ paePath = paeFile.getAbsolutePath();
+ Console.warn(
+ "Problem with the PAE file path: '" + paePath + "'");
+ }
+ String structId = subVals.get("structid");
+ if (subVals.notSet())
+ {
+ // take structid from pdbfilename
+ }
+ if (subVals.has("structfile"))
+ {
+ Console.info("***** Attaching paeFile '" + paePath + "' to "
+ + "structfile=" + subVals.get("structfile"));
+ EBIAlfaFold.addAlphaFoldPAEToStructure(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVals.getIndex(), subVals.get("structfile"), false);
+ }
+ else if (subVals.has("structid"))
+ {
+ Console.info("***** Attaching paeFile '" + paePath + "' to "
+ + "structid=" + subVals.get("structid"));
+ EBIAlfaFold.addAlphaFoldPAEToStructure(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVals.getIndex(), subVals.get("structid"), true);
+ }
+ else
+ {
+ Console.debug("***** Attaching paeFile '" + paePath
+ + "' to sequence index " + subVals.getIndex());
+ EBIAlfaFold.addAlphaFoldPAEToSequence(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVals.getIndex(), null);
+ // required to readjust the height and position of the pAE
+ // annotation
+ }
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ ap.adjustAnnotationHeight();
+ }
+ }
+ }
+ }
+
+ boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
+ if (doShading)
+ {
+ AlignFrame af = afMap.get(id);
+ for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
+ .findAnnotation(PDBChain.class.getName().toString()))
+ {
+ AnnotationColourGradient acg = new AnnotationColourGradient(aa,
+ af.alignPanel.av.getGlobalColourScheme(), 0);
+ acg.setSeqAssociated(true);
+ af.changeColour(acg);
+ Console.info("Changed colour " + acg.toString());
+ }
+ }
}
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)
{
}
}
}
+ // for moment we disable JSON export
+ Cache.setPropsAreReadOnly(true);
+ Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
+
switch (type)
{
case "svg":
}
}
- 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;
}
git://source.jalview.org / jalview.git / blobdiff