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Changed the SCOP Installation URLs #1077

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josemduarte merged 1 commit into from
Jan 25, 2024
Merged

Changed the SCOP Installation URLs #1077

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21 changes: 15 additions & 6 deletions biojava-structure/src/main/java/org/biojava/nbio/structure/scop/ScopInstallation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -85,8 +85,8 @@ public class ScopInstallation implements LocalScopDatabase {
public static final String comFileName = "dir.com.scop.txt_";

// Download locations
public static final String SCOP_DOWNLOAD = "http://scop.berkeley.edu/downloads/parse/";
public static final String SCOP_DOWNLOAD_ALTERNATE = "http://scop.berkeley.edu/downloads/parse/";
public static final String SCOP_DOWNLOAD = "https://scop.berkeley.edu/downloads/parse/";
public static final String SCOP_DOWNLOAD_ALTERNATE = "https://scop.berkeley.edu/downloads/parse/";

//public static final String NEWLINE = System.getProperty("line.separator");
public static final String FILESPLIT = System.getProperty("file.separator");
Expand Down Expand Up @@ -913,10 +913,19 @@ private void initScopURLs() {
// first, try default scop
ScopMirror primary = new ScopMirror();
// If unreachable, try alternate Berkeley location
ScopMirror alt = new ScopMirror(
SCOP_DOWNLOAD_ALTERNATE,
"dir.cla.scop.%s.txt","dir.des.scop.%s.txt",
"dir.hie.scop.%s.txt","dir.com.scop.%s.txt");
ScopMirror alt;
if (scopVersion.startsWith("2.")) {
alt = new ScopMirror(
SCOP_DOWNLOAD_ALTERNATE,
"dir.cla.scope.%s.txt","dir.des.scope.%s.txt",
"dir.hie.scope.%s.txt","dir.com.scope.%s.txt");
}
else {
alt = new ScopMirror(
SCOP_DOWNLOAD_ALTERNATE,
"dir.cla.scop.%s.txt","dir.des.scop.%s.txt",
"dir.hie.scop.%s.txt","dir.com.scop.%s.txt");
}
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@josemduarte josemduarte Jan 8, 2024

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The 2 blocks in the if/else look identical. What was the intention of this change?

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@aalhossary aalhossary Jan 9, 2024

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One is scope while the other is scop.

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@josemduarte josemduarte Jan 10, 2024

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Thanks! sorry I missed that.

mirrors.add(primary);
mirrors.add(alt);
}
Expand Down