import jalview.api.AlignmentViewPanel;
import jalview.bin.ArgParser.Arg;
import jalview.bin.ArgParser.ArgValues;
-import jalview.bin.ArgParser.SubId;
+import jalview.bin.ArgParser.SubVal;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
import jalview.gui.AlignFrame;
import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.io.FileFormatException;
import jalview.io.FileFormatI;
import jalview.io.FileLoader;
+import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
+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;
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())
{
+ Console.debug("##### id=" + id);
Commands cmds = new Commands();
if (id == null)
{
{
cmds.processLinked(id);
}
+ cmds.processImages(id);
+ argsWereParsed |= cmds.wereParsed();
}
+
}
+ 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)
{
+ Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+
processLinked(id);
}
FileFormatI format = null;
DataSourceType protocol = null;
*/
-
- if (m.get(Arg.OPEN) != null)
+ if (ArgParser.getArgValues(m, Arg.OPEN) != null)
{
long progress = -1;
boolean first = true;
AlignFrame af;
- OPEN: for (String openFile : m.get(Arg.OPEN).getValues())
+ for (String openFile : ArgParser.getValues(m, Arg.OPEN))
{
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
- AlignmentAnnotation.TFType tempfacType = null;
- if ((m.get(Arg.NOTEMPFAC) == null
- || !m.get(Arg.NOTEMPFAC).getBoolean())
- && m.get(Arg.TEMPFAC) != null)
+ StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
+ if ((!ArgParser.getBoolean(m, Arg.NOTEMPFAC))
+ && ArgParser.getArgValues(m, Arg.TEMPFAC) != null)
{
try
{
- tempfacType = AlignmentAnnotation.TFType
- .valueOf(m.get(Arg.TEMPFAC).getValue()
- .toUpperCase(Locale.ROOT));
+ tempfacType = StructureImportSettings.TFType.valueOf(ArgParser
+ .getValue(m, Arg.TEMPFAC).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.getName()).append(" to '")
.append(tempfacType)
.append("', ignoring. Valid values are: ");
- Iterator<AlignmentAnnotation.TFType> it = Arrays
- .stream(AlignmentAnnotation.TFType.values())
+ Iterator<StructureImportSettings.TFType> it = Arrays
+ .stream(StructureImportSettings.TFType.values())
.iterator();
while (it.hasNext())
{
Console.debug(
"Opening '" + openFile + "' in new alignment frame");
FileLoader fileLoader = new FileLoader(!headless);
- af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol, format,
- tempfacType);
+
+ StructureImportSettings.setTemperatureFactorType(tempfacType);
+
+ af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
+ format);
// wrap alignment?
- if (m.get(Arg.WRAP) != null && m.get(Arg.WRAP).getBoolean())
+ if (ArgParser.getBoolean(m, Arg.WRAP))
{
af.getCurrentView().setWrapAlignment(true);
}
// change alignment frame title
- if (m.get(Arg.TITLE) != null)
- af.setTitle(m.get(Arg.TITLE).getValue());
+ if (ArgParser.getValue(m, Arg.TITLE) != null)
+ af.setTitle(ArgParser.getValue(m, Arg.TITLE));
/* hacky approach to hiding the annotations */
// show secondary structure annotations?
- if (m.get(Arg.SSANNOTATION) != null)
+ if (ArgParser.getBoolean(m, Arg.SSANNOTATION))
{
- boolean showSS = m.get(Arg.SSANNOTATION).getBoolean();
// do this better (annotation types?)
AlignmentUtils.showOrHideSequenceAnnotations(
af.getCurrentView().getAlignment(),
}
// show temperature factor annotations?
- if (m.get(Arg.NOTEMPFAC) != null
- && m.get(Arg.NOTEMPFAC).getBoolean())
+ if (ArgParser.getBoolean(m, Arg.NOTEMPFAC))
{
// do this better (annotation types?)
List<String> hideThese = new ArrayList<>();
hideThese.add("Temperature Factor");
- hideThese.add(MessageManager
- .getString("label.alphafold_reliability"));
+ hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
AlignmentUtils.showOrHideSequenceAnnotations(
af.getCurrentView().getAlignment(), hideThese, null,
false, false);
if (showTemperatureFactor)
*/
{
- if (m.get(Arg.TEMPFAC_LABEL) != null)
+ if (ArgParser.getValue(m, Arg.TEMPFAC_LABEL) != null)
{
AlignmentAnnotation aa = AlignmentUtils
.getFirstSequenceAnnotationOfType(
af.getCurrentView().getAlignment(),
AlignmentAnnotation.LINE_GRAPH);
- String label = m.get(Arg.TEMPFAC_LABEL).getValue();
+ String label = ArgParser.getValue(m, 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
{
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);
+ // TOREMOVE COMMENT
+ // @Ben assumed this was the GUI version of above, rather then the
+ // first==false state
+ else
+ {
+ Console.warn("No more files to open");
+ if (desktop != null)
+ desktop.setProgressBar(null, progress);
+ }
}
}
// load a pAE file if given
- if (m.get(Arg.PAEMATRIX) != null)
+ if (ArgParser.getValues(m, Arg.PAEMATRIX) != null)
{
AlignFrame af = afMap.get(id);
if (af != null)
{
- for (String val : m.get(Arg.PAEMATRIX).getValues())
+ for (String val : ArgParser.getValues(m, Arg.PAEMATRIX))
{
- SubId subId = ArgParser.getSubId(val);
- File paeFile = new File(subId.content);
- EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, subId.index,
- "id".equals(subId.keyName) ? subId.keyValue : null);
- // required to readjust the height and position of the pAE
- // annotation
+ SubVal subVal = ArgParser.getSubVal(val);
+ File paeFile = new File(subVal.content);
+ String structId = "structid".equals(subVal.keyName)
+ ? subVal.keyValue
+ : null;
+ if (subVal.notSet())
+ {
+ // take structid from pdbfilename
+ }
+ if ("structfile".equals(subVal.keyName))
+ {
+ EBIAlfaFold.addAlphaFoldPAEToStructure(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVal.index, subVal.keyValue, false);
+ }
+ else if ("structid".equals(subVal.keyName))
+ {
+ EBIAlfaFold.addAlphaFoldPAEToStructure(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVal.index, subVal.keyValue, true);
+ }
+ else
+ {
+ EBIAlfaFold.addAlphaFoldPAEToSequence(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVal.index,
+ "seqid".equals(subVal.keyName) ? subVal.keyValue
+ : null);
+ // required to readjust the height and position of the pAE
+ // annotation
+ }
for (AlignmentViewPanel ap : af.getAlignPanels())
{
ap.adjustAnnotationHeight();
}
// open the structure (from same PDB file or given PDBfile)
- if (m.get(Arg.NOSTRUCTURE) == null
- || !m.get(Arg.NOQUESTIONNAIRE).getBoolean())
+ if (!ArgParser.getBoolean(m, Arg.NOSTRUCTURE))
{
AlignFrame af = afMap.get(id);
- if (m.get(Arg.STRUCTURE) != null)
+ if (ArgParser.getArgValues(m, Arg.STRUCTURE) != null)
{
- STRUCTURE: for (String val : m.get(Arg.STRUCTURE).getValues())
+ for (String val : ArgParser.getValues(m, Arg.STRUCTURE))
{
- SubId subId = new SubId(val);
+ SubVal subId = new SubVal(val);
SequenceI seq = getSpecifiedSequence(af, subId);
if (seq == null)
{
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 "
}
}
- private SequenceI getSpecifiedSequence(AlignFrame af, SubId subId)
+ protected void processImages(String id)
{
- SequenceI seq = null;
- SequenceI[] sequences = af.getCurrentView().getAlignment()
- .getSequencesArray();
- if (-1 < subId.index && subId.index < sequences.length)
+ Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+ AlignFrame af = afMap.get(id);
+
+ if (af == null)
{
- seq = sequences[subId.index];
+ Console.warn("Did not have an alignment window for id=" + id);
+ return;
}
- else if ("id".equals(subId.keyName))
+
+ if (ArgParser.getValues(m, Arg.IMAGE) != null)
{
- for (SequenceI s : sequences)
+ for (String val : ArgParser.getValues(m, Arg.IMAGE))
{
- if (s.getDisplayId(false).equals(subId.keyValue))
+ SubVal subVal = new SubVal(val);
+ String type = "png"; // default
+ String fileName = subVal.content;
+ File file = new File(fileName);
+ if ("type".equals(subVal.keyName))
+ {
+ type = subVal.keyValue;
+ }
+ else if (fileName != null)
+ {
+ for (String ext : new String[] { "svg", "png", "html" })
+ {
+ if (fileName.toLowerCase(Locale.ROOT).endsWith("." + ext))
+ {
+ type = ext;
+ }
+ }
+ }
+ // for moment we disable JSON export
+ Cache.setPropsAreReadOnly(true);
+ Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
+
+ switch (type)
{
- seq = s;
+ case "svg":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createSVG(file);
+ break;
+ case "png":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ af.createPNG(file);
+ break;
+ case "html":
+ Console.debug("Outputting type '" + type + "' to " + fileName);
+ HtmlSvgOutput htmlSVG = new HtmlSvgOutput(af.alignPanel);
+ htmlSVG.exportHTML(fileName);
+ break;
+ default:
+ Console.warn("--image type '" + type + "' not known. Ignoring");
break;
}
}
}
- return seq;
+ }
+
+ private SequenceI getSpecifiedSequence(AlignFrame af, SubVal subId)
+ {
+ AlignmentI al = af.getCurrentView().getAlignment();
+ if (-1 < subId.index && subId.index < al.getSequences().size())
+ {
+ return al.getSequenceAt(subId.index);
+ }
+ else if ("id".equals(subId.keyName))
+ {
+ return al.findName(subId.keyValue);
+ }
+ return null;
}
}
git://source.jalview.org / jalview.git / blobdiff