From cfdd7db2ec41aef37264a879ea560e484694351c Mon Sep 17 00:00:00 2001
From: salman <zaher.salman@psi.ch>
Date: Wed, 11 Jan 2023 23:54:19 +0100
Subject: [PATCH] Bug fixes and final modifications.

---
 TrimSPlib.js | 6 ++++--
 TrimSPweb.js | 8 --------
 myplots.js   | 6 ++++--
 3 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/TrimSPlib.js b/TrimSPlib.js
index dc51cb2..204fea5 100644
--- a/TrimSPlib.js
+++ b/TrimSPlib.js
@@ -1194,8 +1194,10 @@ function startSequence(All) {
     writeAsciiFile(seq_file, data);
 
     // Remove the fort.33 and other redundant files
-    cmd="cd " + All["workPath"] + ";rm -f eingabe1.inp; rm -f fort.33";
-    execute(cmd);
+    if (!webOrApp) {
+	cmd="cd " + All["workPath"] + ";rm -f eingabe1.inp; rm -f fort.33";
+	execute(cmd);
+    }
     Progress=100;
     document.getElementById("pBar").style.width = Progress + "%";
     document.getElementById("pBar").innerHTML = Progress + "%";
diff --git a/TrimSPweb.js b/TrimSPweb.js
index 3705990..23508d7 100644
--- a/TrimSPweb.js
+++ b/TrimSPweb.js
@@ -1,17 +1,9 @@
 // This file contains function that are web app specific
-function getFiles(dir, filelist){
-    fileList = [];
-    return fileList;
-}
 
 function execute(command) {
 //    exec(command, {stdio: 'inherit'});
 }
 
-function checkDir(directory) {
-    // Check whether directory exists, if not create it
-    return(1);
-}
 
 function writeAsciiFile(filename,content) {
     // Write string content into ascii file filename
diff --git a/myplots.js b/myplots.js
index 31ea5e6..8dea766 100644
--- a/myplots.js
+++ b/myplots.js
@@ -1,4 +1,6 @@
-const Plotly = require('plotly.js-dist');
+if (!amIWeb()) {
+    const Plotly = require('plotly.js-dist');
+}
 
 function Plot_xy(plotdiv,x,y,labels){
     // Plot (x,y) scatter with x/ylabels
@@ -97,7 +99,7 @@ function sizePlot(){
 
 function resizePl(flag){
     let newx=this.innerWidth/2-50;
-    let newy=this.innerHeight-85;
+    let newy=this.innerHeight-185;
     var plotDiv1=this.document.getElementById("plotRge");
     var plotDiv2=this.document.getElementById("plotFrac");
     var update ={