import java.util.Map;
import jalview.analysis.AlignmentUtils;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.argparser.Arg;
import jalview.bin.argparser.ArgParser;
import jalview.bin.argparser.ArgParser.Position;
import jalview.bin.argparser.ArgValue;
-import jalview.bin.argparser.ArgValues;
import jalview.bin.argparser.ArgValuesMap;
import jalview.bin.argparser.SubVals;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder;
import jalview.gui.AlignFrame;
import jalview.gui.AlignmentPanel;
+import jalview.gui.AppJmol;
import jalview.gui.Desktop;
import jalview.gui.Preferences;
import jalview.gui.StructureChooser;
import jalview.io.NewickFile;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
+import jalview.util.FileUtils;
import jalview.util.HttpUtils;
+import jalview.util.ImageMaker;
+import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.imagemaker.BitmapImageSizing;
public class Commands
{
argParser = argparser;
headless = h;
desktop = d;
- afMap = new HashMap<String, AlignFrame>();
+ afMap = new HashMap<>();
if (argparser != null)
{
processArgs(argparser, headless);
// Show secondary structure annotations?
boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
- Arg.SSANNOTATIONS, av.getSubVals(), null,
+ Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
"STRUCT_FROM_PDB", true);
af.setAnnotationsVisibility(showSSAnnotations, true, false);
af.getCurrentView().getAlignment(), hideThese, null,
false, false);
}
- else
- /*
- * comment out hacky approach up to here and add this line: if
- * (showTemperatureFactor)
- */
- {
- /*
- if (avm.containsArg(Arg.TEMPFAC_LABEL))
- {
- AlignmentAnnotation aa = AlignmentUtils
- .getFirstSequenceAnnotationOfType(
- af.getCurrentView().getAlignment(),
- AlignmentAnnotation.LINE_GRAPH);
- String label = avm.getValue(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);
{
String val = av.getValue();
SubVals subVals = av.getSubVals();
- SequenceI seq = getSpecifiedSequence(af, subVals);
+ SequenceI seq = getSpecifiedSequence(af, avm, av);
if (seq == null)
{
// Could not find sequence from subId, let's assume the first
Console.debug("Using structure file "
+ structureFile.getAbsolutePath());
- // ##### Does this need to happen? Follow
- // openStructureFileForSequence() below
- /*
- PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(structureFile.getAbsolutePath(),
- DataSourceType.FILE, seq, true, Desktop.instance);
- */
-
// open structure view
AlignmentPanel ap = af.alignPanel;
if (headless)
String structureFilepath = structureFile.getAbsolutePath();
// get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
- String paeFilepath = subVals.getWithSubstitutions(argParser, id,
- "paematrix");
- ArgValue paeAv = getArgAssociatedWithStructure(Arg.PAEMATRIX, avm,
- af, structureFilepath);
- if (paeFilepath == null && paeAv != null)
+ String paeFilepath = ArgParser
+ .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
+ Arg.PAEMATRIX, Position.AFTER, av, subVals, null,
+ null, null);
+ if (paeFilepath != null)
{
- SubVals sv = paeAv.getSubVals();
- File paeFile = new File(sv.getContent());
+ File paeFile = new File(paeFilepath);
try
{
// showing annotations from structure file or not
boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm,
- Arg.SSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
+ Arg.SHOWSSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
true);
// get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
// reference annotations
- 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)
- {
- tftString = tftAv.getSubVals().getContent();
- }
- if (tftString != null)
+ String tftString = ArgParser
+ .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
+ Arg.TEMPFAC, Position.AFTER, av, subVals, null,
+ null, null);
+ boolean notempfac = ArgParser.getFromSubValArgOrPref(avm,
+ Arg.NOTEMPFAC, subVals, null, "ADD_TEMPFACT_ANN", false,
+ true);
+ TFType tft = notempfac ? null : TFType.DEFAULT;
+ if (tftString != null && !notempfac)
{
// get kind of temperature factor annotation
try
}
}
- boolean addTempFac = tft != null
- || Cache.getDefault("ADD_TEMPFACT_ANN", false);
-
// TODO use ssFromStructure
- StructureChooser.openStructureFileForSequence(null, null, ap, seq,
- false, structureFilepath, tft, paeFilepath, false,
- ssFromStructure, false, viewerType);
+ StructureViewer sv = StructureChooser
+ .openStructureFileForSequence(null, null, ap, seq, false,
+ structureFilepath, tft, paeFilepath, false,
+ ssFromStructure, false, viewerType);
+
+ if (headless)
+ {
+ sv.setAsync(false);
+ }
+
+ String structureImageFilename = ArgParser.getValueFromSubValOrArg(
+ avm, av, Arg.STRUCTUREIMAGE, subVals);
+ if (sv != null && structureImageFilename != null)
+ {
+ ArgValue siAv = avm.getClosestNextArgValueOfArg(av,
+ Arg.STRUCTUREIMAGE);
+ SubVals sisv = null;
+ if (structureImageFilename.equals(siAv.getValue()))
+ {
+ sisv = siAv.getSubVals();
+ }
+ File structureImageFile = new File(structureImageFilename);
+ String width = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGEWIDTH, sisv);
+ String height = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGEHEIGHT, sisv);
+ String scale = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGESCALE, sisv);
+ String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGETEXTRENDERER, sisv);
+ String typeS = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.STRUCTUREIMAGETYPE, sisv);
+ if (typeS == null || typeS.length() == 0)
+ {
+ typeS = FileUtils.getExtension(structureImageFile);
+ }
+ TYPE imageType;
+ try
+ {
+ imageType = Enum.valueOf(TYPE.class,
+ typeS.toUpperCase(Locale.ROOT));
+ } catch (IllegalArgumentException e)
+ {
+ Console.warn("Do not know image format '" + typeS
+ + "', using PNG");
+ imageType = TYPE.PNG;
+ }
+ BitmapImageSizing userBis = ImageMaker
+ .parseScaleWidthHeightStrings(scale, width, height);
+ switch (StructureViewer.getViewerType())
+ {
+ case JMOL:
+ try
+ {
+ Thread.sleep(1000);
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ JalviewStructureDisplayI sview = sv
+ .getJalviewStructureDisplay();
+ if (sview instanceof AppJmol)
+ {
+ AppJmol jmol = (AppJmol) sview;
+ jmol.makePDBImage(structureImageFile, imageType, renderer,
+ userBis);
+ }
+ break;
+ default:
+ Console.warn("Cannot export image for structure viewer "
+ + sv.getViewerType() + " yet");
+ break;
+ }
+ }
}
}
}
if (renderer == null)
renderer = "text";
String type = "png"; // default
+
+ String scale = ArgParser.getValueFromSubValOrArg(avm, av, Arg.SCALE,
+ subVal);
+ String width = ArgParser.getValueFromSubValOrArg(avm, av, Arg.WIDTH,
+ subVal);
+ String height = ArgParser.getValueFromSubValOrArg(avm, av,
+ Arg.HEIGHT, subVal);
+ BitmapImageSizing userBis = ImageMaker
+ .parseScaleWidthHeightStrings(scale, width, height);
+
type = ArgParser.getValueFromSubValOrArg(avm, av, Arg.TYPE, subVal);
if (type == null && fileName != null)
{
Cache.setPropsAreReadOnly(true);
Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
+ Console.info("Writing " + file);
+
switch (type)
{
case "png":
Console.debug("Outputting type '" + type + "' to " + fileName);
- af.createPNG(file);
+ af.createPNG(file, null, userBis);
break;
case "html":
Console.debug("Setting backups to " + backups);
Cache.applicationProperties.put(BackupFiles.ENABLED,
Boolean.toString(backups));
+
+ Console.info("Writing " + fileName);
+
af.saveAlignment(fileName, ff);
Console.debug("Returning backups to " + savedBackupsPreference);
if (savedBackupsPreference != null)
return true;
}
- private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
+ private SequenceI getSpecifiedSequence(AlignFrame af, ArgValuesMap avm,
+ ArgValue av)
{
- if (subId == null)
+ SubVals subVals = av.getSubVals();
+ ArgValue idAv = avm.getClosestNextArgValueOfArg(av, Arg.SEQID);
+ SequenceI seq = null;
+ if (subVals == null && idAv == null)
return null;
- AlignmentI al = af.getCurrentView().getAlignment();
- if (subId.has("seqid"))
+ if (af == null || af.getCurrentView() == null)
{
- return al.findName(subId.get("seqid"));
+ return null;
}
- else if (-1 < subId.getIndex()
- && subId.getIndex() < al.getSequences().size())
+ AlignmentI al = af.getCurrentView().getAlignment();
+ if (al == null)
{
- return al.getSequenceAt(subId.getIndex());
+ return null;
}
- 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)
+ if (subVals != null)
{
- for (ArgValue av : avm.getArgValueList(arg))
+ if (subVals.has(Arg.SEQID.getName()))
{
- 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();
- }
- }
- }
-
- 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;
- }
+ seq = al.findName(subVals.get(Arg.SEQID.getName()));
}
+ else if (-1 < subVals.getIndex()
+ && subVals.getIndex() < al.getSequences().size())
+ {
+ seq = al.getSequenceAt(subVals.getIndex());
+ }
+ }
+ else if (idAv != null)
+ {
+ seq = al.findName(idAv.getValue());
}
- return null;
+ return seq;
}
}
git://source.jalview.org / jalview.git / blobdiff