package jalview.bin;
import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Locale;
import java.util.Map;
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.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.gui.StructureChooser;
import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
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;
+import jalview.ws.dbsources.EBIAlfaFold;
public class Commands
{
{
argParser = ap;
headless = h;
- for (String id : argParser.linkedIds())
+
+ if (headless)
{
- Commands cmds = new Commands();
- if (id == null)
- {
- cmds.processUnlinked(id);
- }
- else
+ System.setProperty("java.awt.headless", "true");
+ }
+
+ if (argParser != null && argParser.linkedIds() != null)
+ {
+ for (String id : argParser.linkedIds())
{
- cmds.processLinked(id);
+ Console.debug("##### id=" + id);
+ Commands cmds = new Commands();
+ if (id == null)
+ {
+ cmds.processUnlinked(id);
+ }
+ else
+ {
+ cmds.processLinked(id);
+ }
+ cmds.processImages(id);
}
+
+ }
+ if (argParser.getBool(Arg.QUIT))
+ {
+ Jalview.getInstance().quit();
+ // Desktop.instance.quit();
}
}
protected void processUnlinked(String id)
{
+ Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+
processLinked(id);
}
protected void processLinked(String id)
{
Map<Arg, ArgValues> m = argParser.linkedArgs(id);
- FileLoader fileLoader = new FileLoader(!headless);
/*
// script to execute after all loading is completed one way or another
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())
+ OPEN: for (String openFile : ArgParser.getValues(m, Arg.OPEN))
{
if (openFile == null)
continue OPEN;
- Console.debug("********** id = " + id + ", openFile = " + openFile);
if (first)
{
af = afMap.get(id);
if (af == null)
{
+ /*
+ * this approach isn't working yet
+ // get default annotations before opening AlignFrame
+ if (m.get(Arg.SSANNOTATION) != null)
+ {
+ Console.debug("***** SSANNOTATION="
+ + m.get(Arg.SSANNOTATION).getBoolean());
+ }
+ if (m.get(Arg.NOTEMPFAC) != null)
+ {
+ Console.debug(
+ "***** NOTEMPFAC=" + m.get(Arg.NOTEMPFAC).getBoolean());
+ }
+ boolean showSecondaryStructure = (m.get(Arg.SSANNOTATION) != null)
+ ? m.get(Arg.SSANNOTATION).getBoolean()
+ : false;
+ boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null)
+ ? !m.get(Arg.NOTEMPFAC).getBoolean()
+ : false;
+ Console.debug("***** tempfac=" + showTemperatureFactor
+ + ", showSS=" + showSecondaryStructure);
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ if (ssm != null)
+ {
+ ssm.setAddTempFacAnnot(showTemperatureFactor);
+ ssm.setProcessSecondaryStructure(showSecondaryStructure);
+ }
+ */
+
+ // get kind of temperature factor annotation
+ StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
+ if ((!ArgParser.getBoolean(m, Arg.NOTEMPFAC))
+ && ArgParser.getArgValues(m, Arg.TEMPFAC) != null)
+ {
+ try
+ {
+ 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<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);
- if (m.get(Arg.TITLE) != null)
- af.setTitle(m.get(Arg.TITLE).getValue());
- if (m.get(Arg.SSANNOTATION) != null
- && !m.get(Arg.SSANNOTATION).getBoolean())
+
+ // wrap alignment?
+ if (ArgParser.getBoolean(m, Arg.WRAP))
+ {
+ af.getCurrentView().setWrapAlignment(true);
+ }
+
+ // change alignment frame title
+ 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 (ArgParser.getBoolean(m, Arg.SSANNOTATION))
{
// do this better (annotation types?)
AlignmentUtils.showOrHideSequenceAnnotations(
Collections.singleton("Secondary Structure"), null,
false, false);
}
- if (m.get(Arg.NOTEMPFAC) != null
- && m.get(Arg.NOTEMPFAC).getBoolean())
+
+ // show temperature factor annotations?
+ if (ArgParser.getBoolean(m, Arg.NOTEMPFAC))
{
// do this better (annotation types?)
+ List<String> hideThese = new ArrayList<>();
+ hideThese.add("Temperature Factor");
+ hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
AlignmentUtils.showOrHideSequenceAnnotations(
- af.getCurrentView().getAlignment(),
- Collections.singleton("Temperature Factor"), null,
- false, false);
- AlignmentUtils.showOrHideSequenceAnnotations(
- af.getCurrentView().getAlignment(),
- Collections.singleton("Alphafold Reliability"), null,
+ af.getCurrentView().getAlignment(), hideThese, null,
false, false);
}
+ else
+ /* comment out hacky approach up to here and add this line:
+ if (showTemperatureFactor)
+ */
+ {
+ if (ArgParser.getValue(m, Arg.TEMPFAC_LABEL) != null)
+ {
+ AlignmentAnnotation aa = AlignmentUtils
+ .getFirstSequenceAnnotationOfType(
+ af.getCurrentView().getAlignment(),
+ AlignmentAnnotation.LINE_GRAPH);
+ String label = ArgParser.getValue(m, Arg.TEMPFAC_LABEL);
+ if (aa != null)
+ {
+ aa.label = label;
+ }
+ else
+ {
+ Console.info(
+ "Could not find annotation to apply tempfac_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
{
}
}
+
+ // 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))
+ {
+ 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 (!ArgParser.getBoolean(m, Arg.NOSTRUCTURE))
+ {
+ AlignFrame af = afMap.get(id);
+ if (ArgParser.getArgValues(m, Arg.STRUCTURE) != null)
+ {
+ STRUCTURE: for (String val : ArgParser.getValues(m, Arg.STRUCTURE))
+ {
+ SubVal subId = new SubVal(val);
+ SequenceI seq = getSpecifiedSequence(af, subId);
+ if (seq == null)
+ {
+ Console.warn("Could not find sequence for argument --"
+ + Arg.STRUCTURE + "=" + val);
+ break STRUCTURE;
+ }
+ File structureFile = null;
+ if (subId.content != null && subId.content.length() != 0)
+ {
+ structureFile = new File(subId.content);
+ Console.debug("Using structure file (from argument) '"
+ + structureFile.getAbsolutePath() + "'");
+ }
+ /* THIS DOESN'T WORK */
+ else if (seq.getAllPDBEntries() != null
+ && seq.getAllPDBEntries().size() > 0)
+ {
+ structureFile = new File(
+ seq.getAllPDBEntries().elementAt(0).getFile());
+ Console.debug("Using structure file (from sequence) '"
+ + structureFile.getAbsolutePath() + "'");
+ }
+
+ if (structureFile == null)
+ {
+ Console.warn("Not provided structure file with '" + val + "'");
+ continue STRUCTURE;
+ }
+
+ if (!structureFile.exists())
+ {
+ Console.warn("Structure file '"
+ + structureFile.getAbsoluteFile() + "' not found.");
+ continue STRUCTURE;
+ }
+
+ Console.debug("Using structure file "
+ + structureFile.getAbsolutePath());
+
+ // open structure view
+ AlignmentPanel ap = af.alignPanel;
+ StructureChooser.openStructureFileForSequence(ap, seq,
+ structureFile);
+ }
+ }
+ }
+ }
+
+ protected void processImages(String id)
+ {
+ Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+ AlignFrame af = afMap.get(id);
+
+ if (af == null)
+ {
+ Console.warn("Did not have an alignment window for id=" + id);
+ return;
+ }
+
+ if (ArgParser.getValues(m, Arg.IMAGE) != null)
+ {
+ for (String val : ArgParser.getValues(m, Arg.IMAGE))
+ {
+ 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;
+ }
+ }
+ }
+ switch (type)
+ {
+ 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;
+ }
+ }
+ }
}
+ 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