X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FAppletParams.java;h=86546a633d7065cde7dcb3e880d72fd5e7ddf750;hb=d82d17a7ba88f90e6b8b1b591245a7ee70b3975c;hp=290ae0148786eb65b193d5ebbade48e12023295c;hpb=c2f3ff84f6c1fdf4355251cdd0d23703bc452f84;p=jalview.git diff --git a/src/jalview/bin/AppletParams.java b/src/jalview/bin/AppletParams.java index 290ae01..86546a6 100644 --- a/src/jalview/bin/AppletParams.java +++ b/src/jalview/bin/AppletParams.java @@ -1,5 +1,7 @@ package jalview.bin; +import jalview.gui.Preferences; + import java.util.HashMap; import java.util.Map; import java.util.Vector; @@ -15,7 +17,8 @@ public class AppletParams extends HashMap { private final static String[] params = { "alignpdbfiles", - "ANNOTATIONCOLOUR_MAX", "ANNOTATIONCOLOUR_MIN", "annotations", + Preferences.ANNOTATIONCOLOUR_MAX, Preferences.ANNOTATIONCOLOUR_MIN, + "annotations", "APPLICATION_URL", "automaticScrolling", "centrecolumnlabels", "debug", "defaultColour", "defaultColourNuc", "defaultColourProt", "embedded", "enableSplitFrame", "externalstructureviewer", "features", @@ -134,7 +137,18 @@ public class AppletParams extends HashMap switch (appletName) { + // tested, working: + + case "file": + appName = "open"; + value = resourcePath + value; + appletName = null; + break; + case "file2": + value = resourcePath + value; + appName = null; + break; case "jnetfile": value = resourcePath + value; appName = null; @@ -148,7 +162,6 @@ public class AppletParams extends HashMap appName = null; break; case "pdbfile": - appName = "PDBFILE"; value = resourcePath + value; appName = null; break; @@ -158,32 +171,55 @@ public class AppletParams extends HashMap value = resourcePath + value; appletName = null; // taken care of by Jalview break; - // implemented; not tested: - case "annotations": - value = resourcePath + value; - appName = null; - break; case "defaultcolour": - appName = "DEFAULT_COLOUR"; // defaultColour + appName = Preferences.DEFAULT_COLOUR; break; case "defaultcolournuc": - appName = "DEFAULT_COLOUR_NUC";// defaultColourNuc + appName = Preferences.DEFAULT_COLOUR_NUC; break; case "defaultcolourprot": - appName = "DEFAULT_COLOUR_PROT";// defaultColourProt"; + appName = Preferences.DEFAULT_COLOUR_PROT; + break; + + // implemented; not tested: + + case "oninit": + appName = null; + break; + case "annotations": + value = resourcePath + value; + appName = null; break; case "annotationcolour_max": - appName = "ANNOTATIONCOLOUR_MAX"; + appName = Preferences.ANNOTATIONCOLOUR_MAX; break; case "annotationcolour_min": - appName = "ANNOTATIONCOLOUR_MIN"; + appName = Preferences.ANNOTATIONCOLOUR_MIN; + break; + case "enablesplitframe": + appName = Preferences.ENABLE_SPLIT_FRAME; + break; + case "hidefeaturegroups": break; case "centrecolumnlabels": appName = null; break; - case "enablesplitframe": - appName = "enableSplitFrame"; + case "pdbseq": + appName = null; + break; + case "sortby": + appName = Preferences.SORT_ALIGNMENT; // id, etc. + break; + case "sortbytree": + appName = Preferences.SORT_BY_TREE; + value = checkTF(value); + appletName = null; // taken care of by Jalview break; + case "format": + break; + + // probably not relevant: + case "externalstructureviewer": break; case "alignpdbfiles": @@ -197,8 +233,6 @@ public class AppletParams extends HashMap case "heightscale": appName = "heightScale"; break; - case "hidefeaturegroups": - break; case "jalviewhelpurl": break; case "label": @@ -212,26 +246,24 @@ public class AppletParams extends HashMap case "linkurl_": appName = "linkURL_"; break; + case "rgb": + appName = null; // no background for application + break; + + // unknown: + case "nojmol": break; case "normaliselogo": - appName = "normaliseLogo"; + appName = Preferences.NORMALISE_LOGO; break; case "normalisesequencelogo": - appName = "normaliseSequenceLogo"; - break; - case "oninit": - break; - case "pdbseq": - appName = "PDBSEQ"; + appName = Preferences.NORMALISE_CONSENSUS_LOGO; break; case "relaxedidmatch": break; case "resolvetocodebase": break; - case "rgb": - appName = "RGB"; - break; case "scaleproteinascdna": appName = "scaleProteinAsCdna"; break; @@ -239,18 +271,6 @@ public class AppletParams extends HashMap break; case "sequence": break; - case "sortby": - break; - case "sortbytree": - value = checkTF(value); - appletName = null; // taken care of by Jalview - break; - case "format": - break; - case "scorefile": - appName = "scoreFile"; - value = resourcePath + value; - break; case "uppercase": appName = "upperCase"; break; @@ -267,70 +287,69 @@ public class AppletParams extends HashMap appName = "windowWidth"; break; case "wrap": + appName = Preferences.WRAP_ALIGNMENT; break; + case "scorefile": + appName = "scoreFile"; + value = resourcePath + value; + break; + + // TRUE/FALSE - // cases not handled in doc/parameters.xlsx case "debug": value = checkTF(value); break; - case "file": - appName = "open"; - value = resourcePath + value; - break; - case "file2": - value = resourcePath + value; - break; case "embedded": value = checkTF(value); break; - case "showannotation": - appName = "SHOW_ANNOTATIONS"; + case "showbutton": value = checkTF(value); break; - case "showbutton": + case "showannotation": + appName = Preferences.SHOW_ANNOTATIONS; value = checkTF(value); break; case "showconsensus": - appName = "SHOW_CONSENSUS_LOGO"; + appName = Preferences.SHOW_CONSENSUS_LOGO; value = checkTF(value); break; case "showconsensushistogram": - appName = "SHOW_CONSENSUS_HISTOGRAM"; + appName = Preferences.SHOW_CONSENSUS_HISTOGRAM; value = checkTF(value); break; case "showconservation": - appName = "SHOW_CONSERVATION"; + appName = Preferences.SHOW_CONSERVATION; value = checkTF(value); break; - case "showfeaturegroups": + case "showgroupconsensus": + appName = Preferences.SHOW_GROUP_CONSENSUS; value = checkTF(value); break; - case "showfeaturesettings": - appName = "showFeatureSettings"; + case "showgroupconservation": + appName = Preferences.SHOW_GROUP_CONSERVATION; value = checkTF(value); break; - case "showfullid": - appName = "showFullId"; + case "showoccupancy": + appName = Preferences.SHOW_OCCUPANCY; value = checkTF(value); break; - case "showgroupconsensus": - appName = "SHOW_GROUP_CONSENSUS"; + case "showquality": + appName = Preferences.SHOW_QUALITY; value = checkTF(value); break; - case "showgroupconservation": - appName = "SHOW_GROUP_CONSERVATION"; + case "showsequencelogo": + appName = Preferences.SHOW_CONSENSUS_LOGO; value = checkTF(value); break; - case "showoccupancy": - appName = "SHOW_OCCUPANCY"; + case "showfeaturegroups": value = checkTF(value); break; - case "showquality": - appName = "SHOW_QUALITY"; + case "showfeaturesettings": + appName = "showFeatureSettings"; value = checkTF(value); break; - case "showsequencelogo": - appName = "showSequenceLogo"; + case "showfullid": + appName = "showFullId"; value = checkTF(value); break; case "showtreebootstraps": @@ -342,7 +361,7 @@ public class AppletParams extends HashMap value = checkTF(value); break; case "showunconserved": - appName = "showUnconserved"; + appName = Preferences.SHOW_UNCONSERVED; value = checkTF(value); break; case "showunlinkedtreenodes": @@ -350,6 +369,8 @@ public class AppletParams extends HashMap value = checkTF(value); break; default: + // could be pdbFile2, for example + // or one of the app preference names break; } if (value != null)