X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlFile.java;h=92562785557cc57492dace2cab363cadbc99913f;hb=d4271d32477e99e9fbbfa5db3e11f1b79324e60d;hp=72728300b8b1c627631ca6a383cb4b29a2d9e71f;hpb=581e7e5a0736b3b5e5ade54656c194b399b2a3ec;p=jalview.git
diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index 7272830..9256278 100644
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -1,21 +1,54 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
package jalview.io;
-import jalview.gui.AlignFrame;
-import jalview.schemes.ColourSchemeI;
+import jalview.api.ComplexAlignFile;
+import jalview.api.FeatureSettingsModelI;
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceI;
import java.io.IOException;
+import java.io.StringReader;
import org.jsoup.Jsoup;
import org.jsoup.nodes.Document;
import org.jsoup.nodes.Element;
-public class HtmlFile extends AlignFile
+public class HtmlFile extends AlignFile implements ComplexAlignFile
{
public static final String FILE_EXT = "html";
public static final String FILE_DESC = "HTML";
- private ColourSchemeI cs;
+ private String globalColourScheme;
+
+ private boolean showSeqFeatures;
+
+ private HiddenColumns hiddenColumns;
+
+ private SequenceI[] hiddenSequences;
+
+ private FeaturesDisplayedI displayedFeatures;
public HtmlFile()
{
@@ -27,14 +60,17 @@ public class HtmlFile extends AlignFile
super(source);
}
- public HtmlFile(String inFile, String type) throws IOException
+ public HtmlFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
@Override
public void parse() throws IOException
{
+ Element content = null;
+ Document doc = null;
try
{
StringBuilder htmlData = new StringBuilder();
@@ -43,34 +79,116 @@ public class HtmlFile extends AlignFile
{
htmlData.append(currentLine);
}
+ doc = Jsoup.parse(htmlData.toString());
+ } catch (OutOfMemoryError oom)
+ {
+ errormessage = "Not enough memory to process HTML document";
+ throw new IOException(errormessage);
+ }
- Document doc = Jsoup.parse(htmlData.toString());
- Element content = doc.getElementById("seqData");
- String alignmentJsonString = content.val();
+ try
+ {
+ boolean contentFromDiv = true;
+ // search for BioJSON data in div element with id seqData
+ content = doc.select("div[id=seqData]").first();
+ if (content == null)
+ {
+ contentFromDiv = false;
+ // search for BioJSON data in input element with id seqData
+ content = doc.getElementById("seqData");
+ }
- JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
- seqs = jsonFile.seqs;
- seqGroups = jsonFile.seqGroups;
- annotations = jsonFile.annotations;
+ if (content == null)
+ {
+ errormessage = "The html document is not embedded with BioJSON data";
+ throw new IOException(errormessage);
+ }
+ JSONFile jsonFile = new JSONFile().parse(new StringReader(
+ contentFromDiv ? content.text() : content.val()));
+ this.seqs = jsonFile.getSeqs();
+ this.seqGroups = jsonFile.getSeqGroups();
+ this.annotations = jsonFile.getAnnotations();
+ this.showSeqFeatures = jsonFile.isShowSeqFeatures();
+ this.globalColourScheme = jsonFile.getGlobalColourScheme();
+ this.hiddenSequences = jsonFile.getHiddenSequences();
+ this.hiddenColumns = jsonFile.getHiddenColumns();
+ this.displayedFeatures = jsonFile.getDisplayedFeatures();
} catch (Exception e)
{
- e.printStackTrace();
+ throw e;
}
}
- public void LoadAlignmentFeatures(AlignFrame af)
+ @Override
+ public String print(SequenceI[] sqs, boolean jvsuffix)
+ {
+ throw new UnsupportedOperationException(
+ "Print method of HtmlFile is not supported!");
+ }
+
+ @Override
+ public boolean isShowSeqFeatures()
{
- af.setShowSeqFeatures(JSONFile.isSeqFeaturesEnabled());
- af.changeColour(JSONFile.getColourScheme());
- af.setMenusForViewport();
+ return showSeqFeatures;
}
+ public void setShowSeqFeatures(boolean showSeqFeatures)
+ {
+ this.showSeqFeatures = showSeqFeatures;
+ }
@Override
- public String print()
+ public String getGlobalColourScheme()
{
- throw new UnsupportedOperationException(
- "Print method of HtmlFile not yet supported!");
+ return globalColourScheme;
+ }
+
+ public void setColourScheme(String globalColourScheme)
+ {
+ this.globalColourScheme = globalColourScheme;
+ }
+
+ @Override
+ public HiddenColumns getHiddenColumns()
+ {
+ return hiddenColumns;
+ }
+
+ public void setHiddenColumns(HiddenColumns hidden)
+ {
+ this.hiddenColumns = hidden;
+ }
+
+ @Override
+ public SequenceI[] getHiddenSequences()
+ {
+ return hiddenSequences;
+ }
+
+ public void setHiddenSequences(SequenceI[] hiddenSequences)
+ {
+ this.hiddenSequences = hiddenSequences;
+ }
+
+ @Override
+ public FeaturesDisplayedI getDisplayedFeatures()
+ {
+ return displayedFeatures;
+ }
+
+ /**
+ * Returns a descriptor for suitable feature display settings with
+ *
+ * - ResNums or insertions features visible
+ * - insertions features coloured red
+ * - ResNum features coloured by label
+ * - Insertions displayed above (on top of) ResNums
+ *
+ */
+ @Override
+ public FeatureSettingsModelI getFeatureColourScheme()
+ {
+ return new PDBFeatureSettings();
}
}